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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/0501_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/0501_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/0501_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0501_R1.fastp.fq.gz Writing a C -> T converted version of the input file 0501_R1.fastp.fq.gz to 0501_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0501_R1.fastp.fq.gz to 0501_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0501_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0501_R2.fastp.fq.gz Writing a C -> T converted version of the input file 0501_R2.fastp.fq.gz to 0501_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0501_R2.fastp.fq.gz to 0501_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0501_R2.fastp.fq.gz (100001 sequences in total) Input files are 0501_R1.fastp.fq.gz_C_to_T.fastq and 0501_R1.fastp.fq.gz_G_to_A.fastq and 0501_R2.fastp.fq.gz_C_to_T.fastq and 0501_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 0501_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/0501_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/0501_R2.fastp.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99565 (99.56%) aligned concordantly 0 times 262 (0.26%) 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: 99538 (99.54%) aligned concordantly 0 times 291 (0.29%) aligned concordantly exactly 1 time 171 (0.17%) aligned concordantly >1 times 0.46% overall alignment rate 100000 reads; of these: 100000 (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 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 (24.89%) aligned concordantly >1 times 46.87% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 0501_R1.fastp.fq.gz_C_to_T.fastq, 0501_R1.fastp.fq.gz_G_to_A.fastq, 0501_R2.fastp.fq.gz_C_to_T.fastq and 0501_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/0502_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/0502_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/0502_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0502_R1.fastp.fq.gz Writing a C -> T converted version of the input file 0502_R1.fastp.fq.gz to 0502_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0502_R1.fastp.fq.gz to 0502_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0502_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0502_R2.fastp.fq.gz Writing a C -> T converted version of the input file 0502_R2.fastp.fq.gz to 0502_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0502_R2.fastp.fq.gz to 0502_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0502_R2.fastp.fq.gz (100001 sequences in total) Input files are 0502_R1.fastp.fq.gz_C_to_T.fastq and 0502_R1.fastp.fq.gz_G_to_A.fastq and 0502_R2.fastp.fq.gz_C_to_T.fastq and 0502_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 0502_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/0502_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/0502_R2.fastp.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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files 0502_R1.fastp.fq.gz_C_to_T.fastq, 0502_R1.fastp.fq.gz_G_to_A.fastq, 0502_R2.fastp.fq.gz_C_to_T.fastq and 0502_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/0503_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/0503_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/0503_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0503_R1.fastp.fq.gz Writing a C -> T converted version of the input file 0503_R1.fastp.fq.gz to 0503_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0503_R1.fastp.fq.gz to 0503_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0503_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0503_R2.fastp.fq.gz Writing a C -> T converted version of the input file 0503_R2.fastp.fq.gz to 0503_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0503_R2.fastp.fq.gz to 0503_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0503_R2.fastp.fq.gz (100001 sequences in total) Input files are 0503_R1.fastp.fq.gz_C_to_T.fastq and 0503_R1.fastp.fq.gz_G_to_A.fastq and 0503_R2.fastp.fq.gz_C_to_T.fastq and 0503_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 0503_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/0503_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/0503_R2.fastp.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 10000024378 reads; of these: ( 24.38 %100000) aligned concordantly >1 times ( 46.40% overall alignment rate 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.fastp.fq.gz_C_to_T.fastq, 0503_R1.fastp.fq.gz_G_to_A.fastq, 0503_R2.fastp.fq.gz_C_to_T.fastq and 0503_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/3501_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/3501_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/3501_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3501_R1.fastp.fq.gz Writing a C -> T converted version of the input file 3501_R1.fastp.fq.gz to 3501_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3501_R1.fastp.fq.gz to 3501_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3501_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3501_R2.fastp.fq.gz Writing a C -> T converted version of the input file 3501_R2.fastp.fq.gz to 3501_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3501_R2.fastp.fq.gz to 3501_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3501_R2.fastp.fq.gz (100001 sequences in total) Input files are 3501_R1.fastp.fq.gz_C_to_T.fastq and 3501_R1.fastp.fq.gz_G_to_A.fastq and 3501_R2.fastp.fq.gz_C_to_T.fastq and 3501_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 3501_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/3501_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/3501_R2.fastp.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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files 3501_R1.fastp.fq.gz_C_to_T.fastq, 3501_R1.fastp.fq.gz_G_to_A.fastq, 3501_R2.fastp.fq.gz_C_to_T.fastq and 3501_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/3502_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/3502_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/3502_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3502_R1.fastp.fq.gz Writing a C -> T converted version of the input file 3502_R1.fastp.fq.gz to 3502_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3502_R1.fastp.fq.gz to 3502_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3502_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3502_R2.fastp.fq.gz Writing a C -> T converted version of the input file 3502_R2.fastp.fq.gz to 3502_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3502_R2.fastp.fq.gz to 3502_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3502_R2.fastp.fq.gz (100001 sequences in total) Input files are 3502_R1.fastp.fq.gz_C_to_T.fastq and 3502_R1.fastp.fq.gz_G_to_A.fastq and 3502_R2.fastp.fq.gz_C_to_T.fastq and 3502_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 3502_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/3502_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/3502_R2.fastp.fq.gz 100000100000 reads; of these: reads; of these: 100000100000 ( (100.00%) were paired; of these: 99660100.00 (%99.66) were paired; of these:% ) aligned concordantly 0 times 99671 (21599.67 (0.21%%) aligned concordantly 0 times) aligned concordantly exactly 1 time 207125 ( (0.210.12%%) aligned concordantly exactly 1 time) aligned concordantly >1 times 0.34122% ( overall alignment rate0.12 %) aligned concordantly >1 times 0.33% 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 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 Processed 100000 sequences in total Successfully deleted the temporary files 3502_R1.fastp.fq.gz_C_to_T.fastq, 3502_R1.fastp.fq.gz_G_to_A.fastq, 3502_R2.fastp.fq.gz_C_to_T.fastq and 3502_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/3503_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/3503_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/3503_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3503_R1.fastp.fq.gz Writing a C -> T converted version of the input file 3503_R1.fastp.fq.gz to 3503_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3503_R1.fastp.fq.gz to 3503_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3503_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3503_R2.fastp.fq.gz Writing a C -> T converted version of the input file 3503_R2.fastp.fq.gz to 3503_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3503_R2.fastp.fq.gz to 3503_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3503_R2.fastp.fq.gz (100001 sequences in total) Input files are 3503_R1.fastp.fq.gz_C_to_T.fastq and 3503_R1.fastp.fq.gz_G_to_A.fastq and 3503_R2.fastp.fq.gz_C_to_T.fastq and 3503_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 3503_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/3503_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/3503_R2.fastp.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99682 (99.68%) aligned concordantly 0 times 208 (0.21100000% reads; of these:) aligned concordantly exactly 1 time 100000110 ( (0.11%100.00) aligned concordantly >1 times% ) were paired; of these:0.32 % overall alignment rate55137 (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: 99677 (99.68%) aligned concordantly 0 times 198 (0.20%) aligned concordantly exactly 1 time 125 (0.12%) aligned concordantly >1 times 0.32% 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.fastp.fq.gz_C_to_T.fastq, 3503_R1.fastp.fq.gz_G_to_A.fastq, 3503_R2.fastp.fq.gz_C_to_T.fastq and 3503_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/5201_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/5201_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5201_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5201_R1.fastp.fq.gz Writing a C -> T converted version of the input file 5201_R1.fastp.fq.gz to 5201_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5201_R1.fastp.fq.gz to 5201_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5201_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5201_R2.fastp.fq.gz Writing a C -> T converted version of the input file 5201_R2.fastp.fq.gz to 5201_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5201_R2.fastp.fq.gz to 5201_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5201_R2.fastp.fq.gz (100001 sequences in total) Input files are 5201_R1.fastp.fq.gz_C_to_T.fastq and 5201_R1.fastp.fq.gz_G_to_A.fastq and 5201_R2.fastp.fq.gz_C_to_T.fastq and 5201_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 5201_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5201_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5201_R2.fastp.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99505 (99.50%) aligned concordantly 0 times 337 (0.34%) aligned concordantly exactly 1 time 158 (0.16%) aligned concordantly >1 times 0.49% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 52380 (52.38%) aligned concordantly 0 times 22756 (22.76%) aligned concordantly exactly 1 time 24864 (24.86%) aligned concordantly >1 times 47.62% overall alignment rate 100000 reads; of these: 100000 (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 100000 reads; of these: 100000 (100.00%) were paired; of these: 52496 (52.50%) aligned concordantly 0 times 22432 (22.43%) aligned concordantly exactly 1 time 25072 (25.07%) aligned concordantly >1 times 47.50% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 5201_R1.fastp.fq.gz_C_to_T.fastq, 5201_R1.fastp.fq.gz_G_to_A.fastq, 5201_R2.fastp.fq.gz_C_to_T.fastq and 5201_R2.fastp.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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/5202_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/5202_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5202_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5202_R1.fastp.fq.gz Writing a C -> T converted version of the input file 5202_R1.fastp.fq.gz to 5202_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5202_R1.fastp.fq.gz to 5202_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5202_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5202_R2.fastp.fq.gz Writing a C -> T converted version of the input file 5202_R2.fastp.fq.gz to 5202_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5202_R2.fastp.fq.gz to 5202_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5202_R2.fastp.fq.gz (100001 sequences in total) Input files are 5202_R1.fastp.fq.gz_C_to_T.fastq and 5202_R1.fastp.fq.gz_G_to_A.fastq and 5202_R2.fastp.fq.gz_C_to_T.fastq and 5202_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 5202_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5202_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5202_R2.fastp.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: 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: 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: 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.fastp.fq.gz_C_to_T.fastq, 5202_R1.fastp.fq.gz_G_to_A.fastq, 5202_R2.fastp.fq.gz_C_to_T.fastq and 5202_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/5203_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/5203_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5203_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5203_R1.fastp.fq.gz Writing a C -> T converted version of the input file 5203_R1.fastp.fq.gz to 5203_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5203_R1.fastp.fq.gz to 5203_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5203_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5203_R2.fastp.fq.gz Writing a C -> T converted version of the input file 5203_R2.fastp.fq.gz to 5203_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5203_R2.fastp.fq.gz to 5203_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5203_R2.fastp.fq.gz (100001 sequences in total) Input files are 5203_R1.fastp.fq.gz_C_to_T.fastq and 5203_R1.fastp.fq.gz_G_to_A.fastq and 5203_R2.fastp.fq.gz_C_to_T.fastq and 5203_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 5203_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5203_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5203_R2.fastp.fq.gz 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 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: 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 Processed 100000 sequences in total Successfully deleted the temporary files 5203_R1.fastp.fq.gz_C_to_T.fastq, 5203_R1.fastp.fq.gz_G_to_A.fastq, 5203_R2.fastp.fq.gz_C_to_T.fastq and 5203_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/5901_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/5901_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5901_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5901_R1.fastp.fq.gz Writing a C -> T converted version of the input file 5901_R1.fastp.fq.gz to 5901_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5901_R1.fastp.fq.gz to 5901_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5901_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5901_R2.fastp.fq.gz Writing a C -> T converted version of the input file 5901_R2.fastp.fq.gz to 5901_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5901_R2.fastp.fq.gz to 5901_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5901_R2.fastp.fq.gz (100001 sequences in total) Input files are 5901_R1.fastp.fq.gz_C_to_T.fastq and 5901_R1.fastp.fq.gz_G_to_A.fastq and 5901_R2.fastp.fq.gz_C_to_T.fastq and 5901_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 5901_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5901_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5901_R2.fastp.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99638 (99.64%) aligned concordantly 0 times 238 (0.24%) aligned concordantly exactly 1 time 124 (0.12%) aligned concordantly >1 times 0.36% overall alignment rate 100000 reads; of these: 100000 (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 100000 reads; of these: 100000 (100.00%) were paired; of these: 53410 (53.41%) aligned concordantly 0 times 22176 (22.18%) aligned concordantly exactly 1 time 24414 (24.41%) aligned concordantly >1 times 46.59% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 5901_R1.fastp.fq.gz_C_to_T.fastq, 5901_R1.fastp.fq.gz_G_to_A.fastq, 5901_R2.fastp.fq.gz_C_to_T.fastq and 5901_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/5902_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/5902_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5902_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5902_R1.fastp.fq.gz Writing a C -> T converted version of the input file 5902_R1.fastp.fq.gz to 5902_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5902_R1.fastp.fq.gz to 5902_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5902_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5902_R2.fastp.fq.gz Writing a C -> T converted version of the input file 5902_R2.fastp.fq.gz to 5902_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5902_R2.fastp.fq.gz to 5902_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5902_R2.fastp.fq.gz (100001 sequences in total) Input files are 5902_R1.fastp.fq.gz_C_to_T.fastq and 5902_R1.fastp.fq.gz_G_to_A.fastq and 5902_R2.fastp.fq.gz_C_to_T.fastq and 5902_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 5902_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5902_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5902_R2.fastp.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 (100000 reads; of these: 100000 (100.00%) were paired; of these:100.00 % ) were paired; of these:52898 ( 52.9052886% () aligned concordantly 0 times52.89 % ) aligned concordantly 0 times22514 ( 22.5122534% () aligned concordantly exactly 1 time22.53 % ) aligned concordantly exactly 1 time24588 ( 24.5924580% () aligned concordantly >1 times24.58 %47.10) aligned concordantly >1 times% overall alignment rate47.11 % overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 5902_R1.fastp.fq.gz_C_to_T.fastq, 5902_R1.fastp.fq.gz_G_to_A.fastq, 5902_R2.fastp.fq.gz_C_to_T.fastq and 5902_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/5903_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/5903_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5903_R2.fastp.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5903_R1.fastp.fq.gz Writing a C -> T converted version of the input file 5903_R1.fastp.fq.gz to 5903_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5903_R1.fastp.fq.gz to 5903_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5903_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5903_R2.fastp.fq.gz Writing a C -> T converted version of the input file 5903_R2.fastp.fq.gz to 5903_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5903_R2.fastp.fq.gz to 5903_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5903_R2.fastp.fq.gz (100001 sequences in total) Input files are 5903_R1.fastp.fq.gz_C_to_T.fastq and 5903_R1.fastp.fq.gz_G_to_A.fastq and 5903_R2.fastp.fq.gz_C_to_T.fastq and 5903_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and 5903_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5903_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/5903_R2.fastp.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 (53.39%) aligned concordantly 0 times 22194 (22.19%) aligned concordantly exactly 1 time 24415 (24.41%) aligned concordantly >1 times 46.61% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 53584 (53.58%) 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.fastp.fq.gz_C_to_T.fastq, 5903_R1.fastp.fq.gz_G_to_A.fastq, 5903_R2.fastp.fq.gz_C_to_T.fastq and 5903_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_10_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_10_R1.fastp.fq.gz to zr3534_10_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_10_R1.fastp.fq.gz to zr3534_10_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_10_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_10_R2.fastp.fq.gz to zr3534_10_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_10_R2.fastp.fq.gz to zr3534_10_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_10_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3534_10_R1.fastp.fq.gz_C_to_T.fastq and zr3534_10_R1.fastp.fq.gz_G_to_A.fastq and zr3534_10_R2.fastp.fq.gz_C_to_T.fastq and zr3534_10_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_10_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_10_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_10_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_10_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_10_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fastp.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.fastp.fq.gz_C_to_T.fastq, zr3534_10_R1.fastp.fq.gz_G_to_A.fastq, zr3534_10_R2.fastp.fq.gz_C_to_T.fastq and zr3534_10_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_1_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_1_R1.fastp.fq.gz to zr3534_1_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_1_R1.fastp.fq.gz to zr3534_1_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_1_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_1_R2.fastp.fq.gz to zr3534_1_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_1_R2.fastp.fq.gz to zr3534_1_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_1_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3534_1_R1.fastp.fq.gz_C_to_T.fastq and zr3534_1_R1.fastp.fq.gz_G_to_A.fastq and zr3534_1_R2.fastp.fq.gz_C_to_T.fastq and zr3534_1_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_1_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_1_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_1_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_1_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_1_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fastp.fq.gz 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 (14.54%) aligned concordantly >1 times 26.60% 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: 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: 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.fastp.fq.gz_C_to_T.fastq, zr3534_1_R1.fastp.fq.gz_G_to_A.fastq, zr3534_1_R2.fastp.fq.gz_C_to_T.fastq and zr3534_1_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_2_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_2_R1.fastp.fq.gz to zr3534_2_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_2_R1.fastp.fq.gz to zr3534_2_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_2_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_2_R2.fastp.fq.gz to zr3534_2_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_2_R2.fastp.fq.gz to zr3534_2_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_2_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3534_2_R1.fastp.fq.gz_C_to_T.fastq and zr3534_2_R1.fastp.fq.gz_G_to_A.fastq and zr3534_2_R2.fastp.fq.gz_C_to_T.fastq and zr3534_2_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_2_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_2_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_2_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_2_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_2_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fastp.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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3534_2_R1.fastp.fq.gz_C_to_T.fastq, zr3534_2_R1.fastp.fq.gz_G_to_A.fastq, zr3534_2_R2.fastp.fq.gz_C_to_T.fastq and zr3534_2_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_3_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_3_R1.fastp.fq.gz to zr3534_3_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_3_R1.fastp.fq.gz to zr3534_3_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_3_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_3_R2.fastp.fq.gz to zr3534_3_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_3_R2.fastp.fq.gz to zr3534_3_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_3_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3534_3_R1.fastp.fq.gz_C_to_T.fastq and zr3534_3_R1.fastp.fq.gz_G_to_A.fastq and zr3534_3_R2.fastp.fq.gz_C_to_T.fastq and zr3534_3_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_3_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_3_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_3_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_3_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_3_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fastp.fq.gz 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: 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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3534_3_R1.fastp.fq.gz_C_to_T.fastq, zr3534_3_R1.fastp.fq.gz_G_to_A.fastq, zr3534_3_R2.fastp.fq.gz_C_to_T.fastq and zr3534_3_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_4_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_4_R1.fastp.fq.gz to zr3534_4_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_4_R1.fastp.fq.gz to zr3534_4_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_4_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_4_R2.fastp.fq.gz to zr3534_4_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_4_R2.fastp.fq.gz to zr3534_4_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_4_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3534_4_R1.fastp.fq.gz_C_to_T.fastq and zr3534_4_R1.fastp.fq.gz_G_to_A.fastq and zr3534_4_R2.fastp.fq.gz_C_to_T.fastq and zr3534_4_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_4_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_4_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_4_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_4_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_4_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fastp.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: 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 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%100000) aligned concordantly exactly 1 time reads; of these: 14598100000 ( (14.60%) aligned concordantly >1 times100.00 %26.78) were paired; of these:% overall alignment rate 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3534_4_R1.fastp.fq.gz_C_to_T.fastq, zr3534_4_R1.fastp.fq.gz_G_to_A.fastq, zr3534_4_R2.fastp.fq.gz_C_to_T.fastq and zr3534_4_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_5_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_5_R1.fastp.fq.gz to zr3534_5_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_5_R1.fastp.fq.gz to zr3534_5_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_5_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_5_R2.fastp.fq.gz to zr3534_5_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_5_R2.fastp.fq.gz to zr3534_5_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_5_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3534_5_R1.fastp.fq.gz_C_to_T.fastq and zr3534_5_R1.fastp.fq.gz_G_to_A.fastq and zr3534_5_R2.fastp.fq.gz_C_to_T.fastq and zr3534_5_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_5_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_5_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_5_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_5_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_5_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fastp.fq.gz 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 (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: 72961 (72.96%) aligned concordantly 0 times 12130 (12.13%) aligned concordantly exactly 1 time 14909 (14.91%) aligned concordantly >1 times 27.04% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73297 (73.30%) aligned concordantly 0 times 11990 (11.99%) aligned concordantly exactly 1 time 14713 (14.71%) aligned concordantly >1 times 26.70% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_5_R1.fastp.fq.gz_C_to_T.fastq, zr3534_5_R1.fastp.fq.gz_G_to_A.fastq, zr3534_5_R2.fastp.fq.gz_C_to_T.fastq and zr3534_5_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_6_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_6_R1.fastp.fq.gz to zr3534_6_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_6_R1.fastp.fq.gz to zr3534_6_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_6_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_6_R2.fastp.fq.gz to zr3534_6_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_6_R2.fastp.fq.gz to zr3534_6_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_6_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3534_6_R1.fastp.fq.gz_C_to_T.fastq and zr3534_6_R1.fastp.fq.gz_G_to_A.fastq and zr3534_6_R2.fastp.fq.gz_C_to_T.fastq and zr3534_6_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_6_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_6_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_6_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_6_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_6_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fastp.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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3534_6_R1.fastp.fq.gz_C_to_T.fastq, zr3534_6_R1.fastp.fq.gz_G_to_A.fastq, zr3534_6_R2.fastp.fq.gz_C_to_T.fastq and zr3534_6_R2.fastp.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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_7_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_7_R1.fastp.fq.gz to zr3534_7_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_7_R1.fastp.fq.gz to zr3534_7_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_7_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_7_R2.fastp.fq.gz to zr3534_7_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_7_R2.fastp.fq.gz to zr3534_7_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_7_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3534_7_R1.fastp.fq.gz_C_to_T.fastq and zr3534_7_R1.fastp.fq.gz_G_to_A.fastq and zr3534_7_R2.fastp.fq.gz_C_to_T.fastq and zr3534_7_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_7_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_7_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_7_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_7_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_7_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fastp.fq.gz 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: 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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3534_7_R1.fastp.fq.gz_C_to_T.fastq, zr3534_7_R1.fastp.fq.gz_G_to_A.fastq, zr3534_7_R2.fastp.fq.gz_C_to_T.fastq and zr3534_7_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_8_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_8_R1.fastp.fq.gz to zr3534_8_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_8_R1.fastp.fq.gz to zr3534_8_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_8_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_8_R2.fastp.fq.gz to zr3534_8_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_8_R2.fastp.fq.gz to zr3534_8_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_8_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3534_8_R1.fastp.fq.gz_C_to_T.fastq and zr3534_8_R1.fastp.fq.gz_G_to_A.fastq and zr3534_8_R2.fastp.fq.gz_C_to_T.fastq and zr3534_8_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_8_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_8_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_8_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_8_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_8_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fastp.fq.gz 100000 reads; of these: 100000100000 (100000 reads; of these: reads; of these: 100.00 % 100000) were paired; of these:100000 ( ( 72805 (72.81%100.00100.00) aligned concordantly 0 times%% ) were paired; of these:) were paired; of these: 12333 (730267331012.33 ( (%73.0373.31) aligned concordantly exactly 1 time%% ) aligned concordantly 0 times) aligned concordantly 0 times 14862 (122431201914.86 ( (%12.2412.02) aligned concordantly >1 times%% ) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time27.20 % overall alignment rate1473114671 ( (14.7314.67%%) aligned concordantly >1 times) aligned concordantly >1 times 26.9726.69%% overall alignment rate 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3534_8_R1.fastp.fq.gz_C_to_T.fastq, zr3534_8_R1.fastp.fq.gz_G_to_A.fastq, zr3534_8_R2.fastp.fq.gz_C_to_T.fastq and zr3534_8_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_9_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_9_R1.fastp.fq.gz to zr3534_9_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_9_R1.fastp.fq.gz to zr3534_9_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_9_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3534_9_R2.fastp.fq.gz to zr3534_9_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_9_R2.fastp.fq.gz to zr3534_9_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_9_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3534_9_R1.fastp.fq.gz_C_to_T.fastq and zr3534_9_R1.fastp.fq.gz_G_to_A.fastq and zr3534_9_R2.fastp.fq.gz_C_to_T.fastq and zr3534_9_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_9_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_9_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3534_9_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3534_9_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_9_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fastp.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 (100.00%) were paired; of these: 72880 (72.88%) aligned concordantly 0 times 12074100000 ( reads; of these:12.07 % ) aligned concordantly exactly 1 time100000 ( 15046 (15.05%) aligned concordantly >1 times100.00 %27.12) were paired; of these:% overall alignment rate 72879 (72.88%) aligned concordantly 0 times 12263 (12.26%) aligned concordantly exactly 1 time 14858 (14.86%) aligned concordantly >1 times 27.12% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72932 (72.93%) aligned concordantly 0 times 12178 (12.18%) aligned concordantly exactly 1 time 14890 (14.89%) aligned concordantly >1 times 27.07% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72827 (72.83%) aligned concordantly 0 times 12286 (12.29%) aligned concordantly exactly 1 time 14887 (14.89%) aligned concordantly >1 times 27.17% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_9_R1.fastp.fq.gz_C_to_T.fastq, zr3534_9_R1.fastp.fq.gz_G_to_A.fastq, zr3534_9_R2.fastp.fq.gz_C_to_T.fastq and zr3534_9_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_10_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_10_R1.fastp.fq.gz to zr3644_10_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_10_R1.fastp.fq.gz to zr3644_10_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_10_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_10_R2.fastp.fq.gz to zr3644_10_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_10_R2.fastp.fq.gz to zr3644_10_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_10_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_10_R1.fastp.fq.gz_C_to_T.fastq and zr3644_10_R1.fastp.fq.gz_G_to_A.fastq and zr3644_10_R2.fastp.fq.gz_C_to_T.fastq and zr3644_10_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_10_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_10_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_10_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_10_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_10_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fastp.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: 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 100000 reads; of these: 100000 (100.00%) were paired; of these: 72996 (73.00%) aligned concordantly 0 times 12088 (12.09%) aligned concordantly exactly 1 time 14916 (14.92%) aligned concordantly >1 times 27.00% overall alignment rate 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_10_R1.fastp.fq.gz_C_to_T.fastq, zr3644_10_R1.fastp.fq.gz_G_to_A.fastq, zr3644_10_R2.fastp.fq.gz_C_to_T.fastq and zr3644_10_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_11_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_11_R1.fastp.fq.gz to zr3644_11_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_11_R1.fastp.fq.gz to zr3644_11_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_11_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_11_R2.fastp.fq.gz to zr3644_11_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_11_R2.fastp.fq.gz to zr3644_11_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_11_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_11_R1.fastp.fq.gz_C_to_T.fastq and zr3644_11_R1.fastp.fq.gz_G_to_A.fastq and zr3644_11_R2.fastp.fq.gz_C_to_T.fastq and zr3644_11_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_11_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_11_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_11_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_11_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_11_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fastp.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: 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 100000 reads; of these:12011 ( 12.01100000% () aligned concordantly exactly 1 time 15013 (100.0015.01%%) were paired; of these:) aligned concordantly >1 times 27.0272923% ( overall alignment rate72.92 %) aligned concordantly 0 times 12085 (12.09%) aligned concordantly exactly 1 time 14992 (14.99%) aligned concordantly >1 times 27.08% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_11_R1.fastp.fq.gz_C_to_T.fastq, zr3644_11_R1.fastp.fq.gz_G_to_A.fastq, zr3644_11_R2.fastp.fq.gz_C_to_T.fastq and zr3644_11_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_12_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_12_R1.fastp.fq.gz to zr3644_12_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_12_R1.fastp.fq.gz to zr3644_12_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_12_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_12_R2.fastp.fq.gz to zr3644_12_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_12_R2.fastp.fq.gz to zr3644_12_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_12_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_12_R1.fastp.fq.gz_C_to_T.fastq and zr3644_12_R1.fastp.fq.gz_G_to_A.fastq and zr3644_12_R2.fastp.fq.gz_C_to_T.fastq and zr3644_12_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_12_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_12_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_12_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_12_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_12_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fastp.fq.gz 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 100000 reads; of these: 100000 (100.00%) were paired; of these: 73038 (73.04%) aligned concordantly 0 times 12041 (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: 72844 (72.84%) aligned concordantly 0 times 12073 (12.07%) aligned concordantly exactly 1 time 15083 (15.08%) aligned concordantly >1 times 27.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73187 (73.19%) aligned concordantly 0 times 11868 (11.87%) aligned concordantly exactly 1 time 14945 (14.95%) aligned concordantly >1 times 26.81% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_12_R1.fastp.fq.gz_C_to_T.fastq, zr3644_12_R1.fastp.fq.gz_G_to_A.fastq, zr3644_12_R2.fastp.fq.gz_C_to_T.fastq and zr3644_12_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_13_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_13_R1.fastp.fq.gz to zr3644_13_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_13_R1.fastp.fq.gz to zr3644_13_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_13_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_13_R2.fastp.fq.gz to zr3644_13_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_13_R2.fastp.fq.gz to zr3644_13_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_13_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_13_R1.fastp.fq.gz_C_to_T.fastq and zr3644_13_R1.fastp.fq.gz_G_to_A.fastq and zr3644_13_R2.fastp.fq.gz_C_to_T.fastq and zr3644_13_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_13_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_13_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_13_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_13_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_13_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fastp.fq.gz 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: 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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_13_R1.fastp.fq.gz_C_to_T.fastq, zr3644_13_R1.fastp.fq.gz_G_to_A.fastq, zr3644_13_R2.fastp.fq.gz_C_to_T.fastq and zr3644_13_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_14_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_14_R1.fastp.fq.gz to zr3644_14_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_14_R1.fastp.fq.gz to zr3644_14_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_14_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_14_R2.fastp.fq.gz to zr3644_14_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_14_R2.fastp.fq.gz to zr3644_14_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_14_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_14_R1.fastp.fq.gz_C_to_T.fastq and zr3644_14_R1.fastp.fq.gz_G_to_A.fastq and zr3644_14_R2.fastp.fq.gz_C_to_T.fastq and zr3644_14_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_14_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_14_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_14_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_14_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_14_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fastp.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: 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: 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: 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.fastp.fq.gz_C_to_T.fastq, zr3644_14_R1.fastp.fq.gz_G_to_A.fastq, zr3644_14_R2.fastp.fq.gz_C_to_T.fastq and zr3644_14_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_15_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_15_R1.fastp.fq.gz to zr3644_15_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_15_R1.fastp.fq.gz to zr3644_15_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_15_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_15_R2.fastp.fq.gz to zr3644_15_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_15_R2.fastp.fq.gz to zr3644_15_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_15_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_15_R1.fastp.fq.gz_C_to_T.fastq and zr3644_15_R1.fastp.fq.gz_G_to_A.fastq and zr3644_15_R2.fastp.fq.gz_C_to_T.fastq and zr3644_15_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_15_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_15_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_15_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_15_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_15_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fastp.fq.gz 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 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 14898100000 ( reads; of these:14.90 % ) aligned concordantly >1 times100000 (27.06% overall alignment rate 100.00%) were paired; of these: 72976 (72.98%) 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: 73244 (73.24%) aligned concordantly 0 times 11898 (11.90%) aligned concordantly exactly 1 time 14858 (14.86%) aligned concordantly >1 times 26.76% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_15_R1.fastp.fq.gz_C_to_T.fastq, zr3644_15_R1.fastp.fq.gz_G_to_A.fastq, zr3644_15_R2.fastp.fq.gz_C_to_T.fastq and zr3644_15_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_16_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_16_R1.fastp.fq.gz to zr3644_16_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_16_R1.fastp.fq.gz to zr3644_16_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_16_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_16_R2.fastp.fq.gz to zr3644_16_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_16_R2.fastp.fq.gz to zr3644_16_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_16_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_16_R1.fastp.fq.gz_C_to_T.fastq and zr3644_16_R1.fastp.fq.gz_G_to_A.fastq and zr3644_16_R2.fastp.fq.gz_C_to_T.fastq and zr3644_16_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_16_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_16_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_16_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_16_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_16_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fastp.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72878 (72.88%) aligned concordantly 0 times 11931 (11.93%) aligned concordantly exactly 1 time 15191 (15.19%) aligned concordantly >1 times 27.12% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 10000071943 reads; of these: ( 71.94100000% () aligned concordantly 0 times 100.0012366% () were paired; of these:12.37 % ) aligned concordantly exactly 1 time71927 ( 71.9315691% () aligned concordantly 0 times15.69 % ) aligned concordantly >1 times12347 (28.0612.35%% overall alignment rate) 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: 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_16_R1.fastp.fq.gz_C_to_T.fastq, zr3644_16_R1.fastp.fq.gz_G_to_A.fastq, zr3644_16_R2.fastp.fq.gz_C_to_T.fastq and zr3644_16_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_17_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_17_R1.fastp.fq.gz to zr3644_17_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_17_R1.fastp.fq.gz to zr3644_17_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_17_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_17_R2.fastp.fq.gz to zr3644_17_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_17_R2.fastp.fq.gz to zr3644_17_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_17_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_17_R1.fastp.fq.gz_C_to_T.fastq and zr3644_17_R1.fastp.fq.gz_G_to_A.fastq and zr3644_17_R2.fastp.fq.gz_C_to_T.fastq and zr3644_17_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_17_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_17_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_17_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_17_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_17_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fastp.fq.gz 100000 reads; of these: 100000 (100.00100000% reads; of these:) were paired; of these: 10000072285 ( (72.28%) aligned concordantly 0 times 100.0012433% () were paired; of these:12.43 % ) aligned concordantly exactly 1 time72529 ( 72.5315282% () aligned concordantly 0 times15.28 % ) aligned concordantly >1 times12224 (27.7112.22%% overall alignment rate) aligned concordantly exactly 1 time 15247 (15.25%) aligned concordantly >1 times 27.47% 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: 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_17_R1.fastp.fq.gz_C_to_T.fastq, zr3644_17_R1.fastp.fq.gz_G_to_A.fastq, zr3644_17_R2.fastp.fq.gz_C_to_T.fastq and zr3644_17_R2.fastp.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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_18_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_18_R1.fastp.fq.gz to zr3644_18_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_18_R1.fastp.fq.gz to zr3644_18_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_18_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_18_R2.fastp.fq.gz to zr3644_18_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_18_R2.fastp.fq.gz to zr3644_18_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_18_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_18_R1.fastp.fq.gz_C_to_T.fastq and zr3644_18_R1.fastp.fq.gz_G_to_A.fastq and zr3644_18_R2.fastp.fq.gz_C_to_T.fastq and zr3644_18_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_18_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_18_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_18_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_18_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_18_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fastp.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: 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 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: 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_18_R1.fastp.fq.gz_C_to_T.fastq, zr3644_18_R1.fastp.fq.gz_G_to_A.fastq, zr3644_18_R2.fastp.fq.gz_C_to_T.fastq and zr3644_18_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_19_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_19_R1.fastp.fq.gz to zr3644_19_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_19_R1.fastp.fq.gz to zr3644_19_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_19_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_19_R2.fastp.fq.gz to zr3644_19_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_19_R2.fastp.fq.gz to zr3644_19_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_19_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_19_R1.fastp.fq.gz_C_to_T.fastq and zr3644_19_R1.fastp.fq.gz_G_to_A.fastq and zr3644_19_R2.fastp.fq.gz_C_to_T.fastq and zr3644_19_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_19_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_19_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_19_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_19_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_19_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fastp.fq.gz 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 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_19_R1.fastp.fq.gz_C_to_T.fastq, zr3644_19_R1.fastp.fq.gz_G_to_A.fastq, zr3644_19_R2.fastp.fq.gz_C_to_T.fastq and zr3644_19_R2.fastp.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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_1_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_1_R1.fastp.fq.gz to zr3644_1_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_1_R1.fastp.fq.gz to zr3644_1_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_1_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_1_R2.fastp.fq.gz to zr3644_1_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_1_R2.fastp.fq.gz to zr3644_1_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_1_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_1_R1.fastp.fq.gz_C_to_T.fastq and zr3644_1_R1.fastp.fq.gz_G_to_A.fastq and zr3644_1_R2.fastp.fq.gz_C_to_T.fastq and zr3644_1_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_1_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_1_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_1_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_1_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_1_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fastp.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.fastp.fq.gz_C_to_T.fastq, zr3644_1_R1.fastp.fq.gz_G_to_A.fastq, zr3644_1_R2.fastp.fq.gz_C_to_T.fastq and zr3644_1_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_20_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_20_R1.fastp.fq.gz to zr3644_20_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_20_R1.fastp.fq.gz to zr3644_20_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_20_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_20_R2.fastp.fq.gz to zr3644_20_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_20_R2.fastp.fq.gz to zr3644_20_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_20_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_20_R1.fastp.fq.gz_C_to_T.fastq and zr3644_20_R1.fastp.fq.gz_G_to_A.fastq and zr3644_20_R2.fastp.fq.gz_C_to_T.fastq and zr3644_20_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_20_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_20_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_20_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_20_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_20_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fastp.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: 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: 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: 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.fastp.fq.gz_C_to_T.fastq, zr3644_20_R1.fastp.fq.gz_G_to_A.fastq, zr3644_20_R2.fastp.fq.gz_C_to_T.fastq and zr3644_20_R2.fastp.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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_21_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_21_R1.fastp.fq.gz to zr3644_21_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_21_R1.fastp.fq.gz to zr3644_21_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_21_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_21_R2.fastp.fq.gz to zr3644_21_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_21_R2.fastp.fq.gz to zr3644_21_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_21_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_21_R1.fastp.fq.gz_C_to_T.fastq and zr3644_21_R1.fastp.fq.gz_G_to_A.fastq and zr3644_21_R2.fastp.fq.gz_C_to_T.fastq and zr3644_21_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_21_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_21_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_21_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_21_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_21_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fastp.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: 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 12127100000 ( reads; of these:12.13 % ) aligned concordantly exactly 1 time100000 ( 14740 (100.0014.74%%) were paired; of these:) aligned concordantly >1 times 26.8772946% ( overall alignment rate72.95 %) 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_21_R1.fastp.fq.gz_C_to_T.fastq, zr3644_21_R1.fastp.fq.gz_G_to_A.fastq, zr3644_21_R2.fastp.fq.gz_C_to_T.fastq and zr3644_21_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_22_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_22_R1.fastp.fq.gz to zr3644_22_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_22_R1.fastp.fq.gz to zr3644_22_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_22_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_22_R2.fastp.fq.gz to zr3644_22_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_22_R2.fastp.fq.gz to zr3644_22_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_22_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_22_R1.fastp.fq.gz_C_to_T.fastq and zr3644_22_R1.fastp.fq.gz_G_to_A.fastq and zr3644_22_R2.fastp.fq.gz_C_to_T.fastq and zr3644_22_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_22_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_22_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_22_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_22_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_22_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fastp.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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_22_R1.fastp.fq.gz_C_to_T.fastq, zr3644_22_R1.fastp.fq.gz_G_to_A.fastq, zr3644_22_R2.fastp.fq.gz_C_to_T.fastq and zr3644_22_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_23_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_23_R1.fastp.fq.gz to zr3644_23_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_23_R1.fastp.fq.gz to zr3644_23_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_23_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_23_R2.fastp.fq.gz to zr3644_23_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_23_R2.fastp.fq.gz to zr3644_23_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_23_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_23_R1.fastp.fq.gz_C_to_T.fastq and zr3644_23_R1.fastp.fq.gz_G_to_A.fastq and zr3644_23_R2.fastp.fq.gz_C_to_T.fastq and zr3644_23_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_23_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_23_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_23_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_23_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_23_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fastp.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: 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: 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: 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.fastp.fq.gz_C_to_T.fastq, zr3644_23_R1.fastp.fq.gz_G_to_A.fastq, zr3644_23_R2.fastp.fq.gz_C_to_T.fastq and zr3644_23_R2.fastp.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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_24_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_24_R1.fastp.fq.gz to zr3644_24_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_24_R1.fastp.fq.gz to zr3644_24_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_24_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_24_R2.fastp.fq.gz to zr3644_24_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_24_R2.fastp.fq.gz to zr3644_24_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_24_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_24_R1.fastp.fq.gz_C_to_T.fastq and zr3644_24_R1.fastp.fq.gz_G_to_A.fastq and zr3644_24_R2.fastp.fq.gz_C_to_T.fastq and zr3644_24_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_24_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_24_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_24_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_24_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_24_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fastp.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: 72676 (72.68%) aligned concordantly 0 times 12467 (12.47%) aligned concordantly exactly 1 time 14857 (14.86%) aligned concordantly >1 times 27.32% 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 (100.00%) were paired; of these: 73038 (73.04%) aligned concordantly 0 times 12142 (12.14%) aligned concordantly exactly 1 time 14820 (14.82%) aligned concordantly >1 times 26.96% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_24_R1.fastp.fq.gz_C_to_T.fastq, zr3644_24_R1.fastp.fq.gz_G_to_A.fastq, zr3644_24_R2.fastp.fq.gz_C_to_T.fastq and zr3644_24_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_2_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_2_R1.fastp.fq.gz to zr3644_2_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_2_R1.fastp.fq.gz to zr3644_2_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_2_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_2_R2.fastp.fq.gz to zr3644_2_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_2_R2.fastp.fq.gz to zr3644_2_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_2_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_2_R1.fastp.fq.gz_C_to_T.fastq and zr3644_2_R1.fastp.fq.gz_G_to_A.fastq and zr3644_2_R2.fastp.fq.gz_C_to_T.fastq and zr3644_2_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_2_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_2_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_2_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_2_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_2_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fastp.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: 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 reads; of these:100000 ( 100000 (100.00%) were paired; of these:100.00 % ) were paired; of these:73184 ( 73.1873278% () aligned concordantly 0 times73.28 % ) aligned concordantly 0 times12163 ( 12.1612041% () aligned concordantly exactly 1 time12.04 % ) aligned concordantly exactly 1 time14653 ( 14.6514681% () aligned concordantly >1 times14.68 %26.82) aligned concordantly >1 times% overall alignment rate26.72 % overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_2_R1.fastp.fq.gz_C_to_T.fastq, zr3644_2_R1.fastp.fq.gz_G_to_A.fastq, zr3644_2_R2.fastp.fq.gz_C_to_T.fastq and zr3644_2_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_3_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_3_R1.fastp.fq.gz to zr3644_3_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_3_R1.fastp.fq.gz to zr3644_3_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_3_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_3_R2.fastp.fq.gz to zr3644_3_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_3_R2.fastp.fq.gz to zr3644_3_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_3_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_3_R1.fastp.fq.gz_C_to_T.fastq and zr3644_3_R1.fastp.fq.gz_G_to_A.fastq and zr3644_3_R2.fastp.fq.gz_C_to_T.fastq and zr3644_3_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_3_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_3_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_3_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_3_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_3_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fastp.fq.gz 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: 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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_3_R1.fastp.fq.gz_C_to_T.fastq, zr3644_3_R1.fastp.fq.gz_G_to_A.fastq, zr3644_3_R2.fastp.fq.gz_C_to_T.fastq and zr3644_3_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_4_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_4_R1.fastp.fq.gz to zr3644_4_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_4_R1.fastp.fq.gz to zr3644_4_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_4_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_4_R2.fastp.fq.gz to zr3644_4_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_4_R2.fastp.fq.gz to zr3644_4_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_4_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_4_R1.fastp.fq.gz_C_to_T.fastq and zr3644_4_R1.fastp.fq.gz_G_to_A.fastq and zr3644_4_R2.fastp.fq.gz_C_to_T.fastq and zr3644_4_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_4_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_4_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_4_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_4_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_4_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fastp.fq.gz 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: 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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_4_R1.fastp.fq.gz_C_to_T.fastq, zr3644_4_R1.fastp.fq.gz_G_to_A.fastq, zr3644_4_R2.fastp.fq.gz_C_to_T.fastq and zr3644_4_R2.fastp.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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_5_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_5_R1.fastp.fq.gz to zr3644_5_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_5_R1.fastp.fq.gz to zr3644_5_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_5_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_5_R2.fastp.fq.gz to zr3644_5_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_5_R2.fastp.fq.gz to zr3644_5_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_5_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_5_R1.fastp.fq.gz_C_to_T.fastq and zr3644_5_R1.fastp.fq.gz_G_to_A.fastq and zr3644_5_R2.fastp.fq.gz_C_to_T.fastq and zr3644_5_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_5_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_5_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_5_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_5_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_5_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fastp.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: 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: 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: 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 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 Processed 100000 sequences in total Successfully deleted the temporary files zr3644_5_R1.fastp.fq.gz_C_to_T.fastq, zr3644_5_R1.fastp.fq.gz_G_to_A.fastq, zr3644_5_R2.fastp.fq.gz_C_to_T.fastq and zr3644_5_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_6_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_6_R1.fastp.fq.gz to zr3644_6_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_6_R1.fastp.fq.gz to zr3644_6_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_6_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_6_R2.fastp.fq.gz to zr3644_6_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_6_R2.fastp.fq.gz to zr3644_6_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_6_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_6_R1.fastp.fq.gz_C_to_T.fastq and zr3644_6_R1.fastp.fq.gz_G_to_A.fastq and zr3644_6_R2.fastp.fq.gz_C_to_T.fastq and zr3644_6_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_6_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_6_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_6_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_6_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_6_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fastp.fq.gz 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: 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: 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: 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.fastp.fq.gz_C_to_T.fastq, zr3644_6_R1.fastp.fq.gz_G_to_A.fastq, zr3644_6_R2.fastp.fq.gz_C_to_T.fastq and zr3644_6_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_7_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_7_R1.fastp.fq.gz to zr3644_7_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_7_R1.fastp.fq.gz to zr3644_7_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_7_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_7_R2.fastp.fq.gz to zr3644_7_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_7_R2.fastp.fq.gz to zr3644_7_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_7_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_7_R1.fastp.fq.gz_C_to_T.fastq and zr3644_7_R1.fastp.fq.gz_G_to_A.fastq and zr3644_7_R2.fastp.fq.gz_C_to_T.fastq and zr3644_7_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_7_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_7_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_7_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_7_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_7_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fastp.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73442 (73.44%) 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: 73194 (73.19%) aligned concordantly 0 times 11972 (11.97%) aligned concordantly exactly 1 time 14834 (14.83%) aligned concordantly >1 times 26.81% overall alignment rate 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: 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.fastp.fq.gz_C_to_T.fastq, zr3644_7_R1.fastp.fq.gz_G_to_A.fastq, zr3644_7_R2.fastp.fq.gz_C_to_T.fastq and zr3644_7_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_8_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_8_R1.fastp.fq.gz to zr3644_8_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_8_R1.fastp.fq.gz to zr3644_8_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_8_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_8_R2.fastp.fq.gz to zr3644_8_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_8_R2.fastp.fq.gz to zr3644_8_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_8_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_8_R1.fastp.fq.gz_C_to_T.fastq and zr3644_8_R1.fastp.fq.gz_G_to_A.fastq and zr3644_8_R2.fastp.fq.gz_C_to_T.fastq and zr3644_8_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_8_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_8_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_8_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_8_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_8_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fastp.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 100000 reads; of these: 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 100000 reads; of these: 100000 (100.00%) were paired; of these: 72716 (72.72%) aligned concordantly 0 times 12010 (12.01%) aligned concordantly exactly 1 time 15274 (15.27%) aligned concordantly >1 times 27.28% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72891 (72.89%) aligned concordantly 0 times 11910 (11.91%) aligned concordantly exactly 1 time 15199 (15.20%) 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 27.27% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_8_R1.fastp.fq.gz_C_to_T.fastq, zr3644_8_R1.fastp.fq.gz_G_to_A.fastq, zr3644_8_R2.fastp.fq.gz_C_to_T.fastq and zr3644_8_R2.fastp.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 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/sr320/060821-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_9_R1.fastp.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fastp.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/sr320/060821-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.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fastp.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.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_9_R1.fastp.fq.gz to zr3644_9_R1.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_9_R1.fastp.fq.gz to zr3644_9_R1.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_9_R1.fastp.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fastp.fq.gz Writing a C -> T converted version of the input file zr3644_9_R2.fastp.fq.gz to zr3644_9_R2.fastp.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_9_R2.fastp.fq.gz to zr3644_9_R2.fastp.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_9_R2.fastp.fq.gz (100001 sequences in total) Input files are zr3644_9_R1.fastp.fq.gz_C_to_T.fastq and zr3644_9_R1.fastp.fq.gz_G_to_A.fastq and zr3644_9_R2.fastp.fq.gz_C_to_T.fastq and zr3644_9_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_9_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_9_R2.fastp.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.fastp.fq.gz_G_to_A.fastq and zr3644_9_R2.fastp.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.fastp.fq.gz_C_to_T.fastq and zr3644_9_R2.fastp.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.fastp_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_9_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fastp.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72015 (72.02%) aligned concordantly 0 times 12145 (12.14%) aligned concordantly exactly 1 time 15840 (15.84%) aligned concordantly >1 times 27.98% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72552 (72.55%) aligned concordantly 0 times 11928 (11.93%) aligned concordantly exactly 1 time 15520 (15.52%) aligned concordantly >1 times 27.45% overall alignment rate 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 (100.00%) were paired; of these: 72275 (72.28%) aligned concordantly 0 times 12045 (12.04%) aligned concordantly exactly 1 time 15680 (15.68%) aligned concordantly >1 times 27.73% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_9_R1.fastp.fq.gz_C_to_T.fastq, zr3644_9_R1.fastp.fq.gz_G_to_A.fastq, zr3644_9_R2.fastp.fq.gz_C_to_T.fastq and zr3644_9_R2.fastp.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 49s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): 0501_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 0501_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 0501_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0501_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 0502_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 0502_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 0502_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0502_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 0503_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 0503_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 0503_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0503_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 3501_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 3501_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 3501_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3501_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 3502_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 3502_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 3502_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3502_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 3503_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 3503_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 3503_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3503_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5201_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5201_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5201_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5201_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5202_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5202_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5202_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5202_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5203_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5203_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5203_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5203_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5901_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5901_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5901_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5901_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5902_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5902_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5902_R1.fastp_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.fastp_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 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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/5902_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5902_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5903_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5903_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5903_R1.fastp_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 5903_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5903_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_10_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_10_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_1_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_1_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_2_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_2_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_3_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_3_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_4_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_4_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_5_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_5_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_6_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_6_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_7_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_7_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_8_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_8_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_9_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_9_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_10_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_10_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_11_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_11_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_12_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_12_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_13_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_13_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_14_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_14_R1.fastp_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.fastp_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 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_14_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_15_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_15_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_16_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_16_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_17_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_17_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_18_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_18_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_19_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_19_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_1_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_1_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_20_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_20_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_21_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_21_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_22_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_22_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_23_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_23_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_24_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_24_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_2_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_2_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_3_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_3_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_4_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_4_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_5_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_5_R1.fastp_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.fastp_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 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_5_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_6_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_6_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_7_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_7_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_8_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_8_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fastp.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_9_R1.fastp_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.fastp_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_9_R1.fastp_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.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fastp.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.fastp_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/sr320/060821-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.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >0501_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_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/0501_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0501_R2.fastp.fq.gz" Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bam 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: '0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 0501_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 0501_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 0501_R1.fastp_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/sr320/060821-bigC/CpG_OT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 0501_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 0501_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_0501_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 0501_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>0502_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >0502_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0502_R1.fastp_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 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0502_R1.fastp_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 0502_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0502_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0502_R2.fastp.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: '0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 0502_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 0502_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 0502_R1.fastp_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/sr320/060821-bigC/CpG_OT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 0502_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 0502_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_0502_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 0502_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>0503_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >0503_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0503_R1.fastp_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/0503_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0503_R2.fastp.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: '0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 0503_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 0503_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 0503_R1.fastp_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/sr320/060821-bigC/CpG_OT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 0503_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 0503_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_0503_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 0503_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>3501_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >3501_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3501_R1.fastp_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 3501_R1.fastp_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/3501_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3501_R2.fastp.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: '3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 3501_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 3501_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 3501_R1.fastp_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/sr320/060821-bigC/CpG_OT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 3501_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 3501_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_3501_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 3501_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>3502_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >3502_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3502_R1.fastp_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 3502_R1.fastp_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 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 Warning: unable to close filehandle IN properly. 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 3502_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3502_R2.fastp.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: '3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 3502_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 3502_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 3502_R1.fastp_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/sr320/060821-bigC/CpG_OT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 3502_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 3502_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_3502_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 3502_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>3503_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >3503_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3503_R1.fastp_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 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3503_R1.fastp_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 3503_R1.fastp_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/3503_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3503_R2.fastp.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: '3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 3503_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 3503_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 3503_R1.fastp_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/sr320/060821-bigC/CpG_OT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 3503_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 3503_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_3503_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 3503_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5201_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5201_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1.fastp_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/5201_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5201_R2.fastp.fq.gz" Now reading in Bismark result file 5201_R1.fastp_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.. 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: '5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5201_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5201_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5201_R1.fastp_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/sr320/060821-bigC/CpG_OT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5201_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5201_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5201_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5201_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5202_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5202_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1.fastp_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/5202_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5202_R2.fastp.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: '5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5202_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5202_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5202_R1.fastp_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/sr320/060821-bigC/CpG_OT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5202_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5202_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5202_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5202_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5203_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5203_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5203_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5203_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5203_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5203_R2.fastp.fq.gz" Now reading in Bismark result file 5203_R1.fastp_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.. 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: '5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5203_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5203_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5203_R1.fastp_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/sr320/060821-bigC/CpG_OT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5203_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5203_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5203_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5203_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5901_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5901_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5901_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5901_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5901_R2.fastp.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: '5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5901_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5901_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5901_R1.fastp_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/sr320/060821-bigC/CpG_OT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5901_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5901_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5901_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5901_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5902_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5902_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_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 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5902_R1.fastp_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/5902_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5902_R2.fastp.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: '5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5902_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5902_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5902_R1.fastp_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/sr320/060821-bigC/CpG_OT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5902_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5902_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5902_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5902_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5903_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5903_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5903_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5903_R2.fastp.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: '5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5903_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5903_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5903_R1.fastp_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/sr320/060821-bigC/CpG_OT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5903_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5903_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5903_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5903_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_10_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fastp.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: 'zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_10_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_10_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_10_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_10_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_1_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_1_R1.fastp_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_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_1_R1.fastp_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.fastp_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 Now reading in Bismark result file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fastp.fq.gz" 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.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_1_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_1_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_1_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_1_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_2_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_2_R1.fastp_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_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_2_R1.fastp_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_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_2_R1.fastp_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_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp_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_2_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fastp.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.. 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: 'zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_2_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_2_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_2_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_2_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_3_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_3_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp_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 Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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 Now reading in Bismark result file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 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/zr3534_3_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fastp.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_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_3_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_3_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_3_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_3_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_4_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_4_R1.fastp_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/zr3534_4_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fastp.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: 'zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_4_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_4_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_4_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_4_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_5_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_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_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_5_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fastp.fq.gz" Now reading in Bismark result file zr3534_5_R1.fastp_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.. 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_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_5_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_5_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_5_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_5_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_6_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_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_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fastp.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: 'zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_6_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_6_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_6_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_6_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_7_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_7_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_7_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fastp.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: 'zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_7_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_7_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_7_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_7_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_8_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fastp.fq.gz" Now reading in Bismark result file zr3534_8_R1.fastp_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.. 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: 'zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_8_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_8_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_8_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_8_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_9_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_9_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp_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 Now reading in Bismark result file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bam 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/zr3534_9_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fastp.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_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_9_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_9_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_9_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_9_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_10_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_10_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_10_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fastp.fq.gz" Now reading in Bismark result file zr3644_10_R1.fastp_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_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_10_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_10_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_10_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_10_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_11_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_11_R1.fastp_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.fastp_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_11_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fastp.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: 'zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_11_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_11_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_11_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_11_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_12_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_12_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_12_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1.fastp_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_12_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fastp.fq.gz" Now reading in Bismark result file zr3644_12_R1.fastp_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: 'zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_12_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_12_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_12_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_12_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_13_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1.fastp_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 Now reading in Bismark result file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fastp.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: 'zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_13_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_13_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_13_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_13_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_14_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1.fastp_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 Now reading in Bismark result file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fastp.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: 'zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_14_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_14_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_14_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_14_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_15_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fastp.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: 'zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_15_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_15_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_15_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_15_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_16_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_16_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_16_R1.fastp_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.fastp_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 Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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 Now reading in Bismark result file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bam 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fastp.fq.gz" 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.. 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_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_16_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_16_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_16_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_16_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_17_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_17_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1.fastp_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 Now reading in Bismark result file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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_17_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fastp.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: 'zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_17_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_17_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_17_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_17_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_18_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_18_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_18_R1.fastp_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 Now reading in Bismark result file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fastp.fq.gz" Now reading in Bismark result file zr3644_18_R1.fastp_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: 'zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_18_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_18_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_18_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_18_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_19_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1.fastp_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.fastp_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 Now reading in Bismark result file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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_19_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fastp.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: 'zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_19_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_19_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_19_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_19_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_1_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_1_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1.fastp_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 Warning: unable to close filehandle IN properly. 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fastp.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: 'zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_1_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_1_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_1_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_1_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_20_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_20_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_20_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fastp.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_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_20_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_20_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_20_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_20_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_21_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_21_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fastp.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. 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Merging individual splitting reports into overall report: 'zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_21_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_21_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_21_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_21_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_22_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_22_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_22_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fastp.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: 'zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_22_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_22_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_22_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_22_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_23_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_23_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_23_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_23_R1.fastp_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_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1.fastp_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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fastp.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.. 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Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_23_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_23_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_23_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_23_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_24_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_24_R1.fastp_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.fastp_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_24_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fastp.fq.gz" Now reading in Bismark result file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1.fastp_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: 'zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_24_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_24_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_24_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_24_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_2_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1.fastp_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 Now reading in Bismark result file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fastp.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: 'zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_2_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_2_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_2_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_2_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_3_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_3_R1.fastp_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_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_3_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1.fastp_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_3_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fastp.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_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_3_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_3_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_3_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_3_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_4_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_4_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_4_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1.fastp_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 Now reading in Bismark result file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fastp.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: 'zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_4_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_4_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_4_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_4_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_5_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_5_R1.fastp_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.fastp_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_5_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fastp.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: 'zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_5_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_5_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_5_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_5_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_6_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1.fastp_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 Now reading in Bismark result file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. 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_6_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fastp.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: 'zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_6_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_6_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_6_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_6_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_7_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_7_R1.fastp_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_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_7_R1.fastp_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_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1.fastp_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_7_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fastp.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: 'zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_7_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_7_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_7_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_7_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_8_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_8_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_8_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_8_R1.fastp_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 Now reading in Bismark result file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bam 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 Warning: unable to close filehandle IN properly. 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.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fastp.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: 'zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_8_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_8_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_8_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_8_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_9_R1.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1.fastp_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_9_R1.fastp.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fastp.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: 'zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_9_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_9_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_9_R1.fastp_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/sr320/060821-bigC/CpG_OT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_CTOB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060821-bigC/CpG_OB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_9_R1.fastp_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.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 46 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> 0501_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 0501_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 0501_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 0501_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 0501_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 0501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 0501_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 0501_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 0502_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 0502_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 0502_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 0502_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 0502_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 0502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 0502_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 0502_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 0503_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 0503_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 0503_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 0503_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 0503_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 0503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 0503_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 0503_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 3501_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 3501_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 3501_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 3501_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 3501_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 3501_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 3501_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 3501_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 3502_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 3502_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 3502_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 3502_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 3502_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 3502_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 3502_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 3502_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 3503_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 3503_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 3503_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 3503_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 3503_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 3503_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 3503_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 3503_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5201_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5201_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 5201_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5201_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5201_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5201_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5201_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5201_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5202_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5202_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 5202_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5202_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5202_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5202_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5202_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5202_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5203_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5203_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 5203_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5203_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5203_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5203_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5203_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5203_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5901_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5901_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 5901_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5901_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5901_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5901_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5901_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5901_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5902_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5902_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 5902_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5902_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5902_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5902_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5902_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5902_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5903_R1.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5903_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report 5903_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5903_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5903_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5903_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5903_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5903_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_10_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3534_10_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_10_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_10_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_10_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_1_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3534_1_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_1_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_1_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_1_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_2_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3534_2_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_2_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_2_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_2_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_3_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3534_3_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_3_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_3_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_3_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_4_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3534_4_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_4_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_4_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_4_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_5_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3534_5_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_5_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_5_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_5_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_6_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3534_6_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_6_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_6_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_6_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_7_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3534_7_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_7_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_7_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_7_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_8_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3534_8_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_8_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_8_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_8_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_9_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3534_9_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_9_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_9_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_9_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_10_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_10_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_10_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_10_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_10_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_11_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_11_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_11_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_11_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_11_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_12_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_12_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_12_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_12_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_12_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_13_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_13_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_13_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_13_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_13_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_14_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_14_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_14_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_14_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_14_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_15_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_15_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_15_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_15_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_15_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_16_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_16_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_16_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_16_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_16_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_17_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_17_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_17_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_17_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_17_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_18_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_18_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_18_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_18_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_18_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_19_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_19_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_19_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_19_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_19_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_1_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_1_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_1_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_1_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_1_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_20_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_20_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_20_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_20_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_20_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_21_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_21_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_21_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_21_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_21_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_22_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_22_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_22_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_22_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_22_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_23_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_23_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_23_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_23_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_23_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_24_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_24_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_24_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_24_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_24_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_2_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_2_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_2_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_2_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_2_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_3_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_3_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_3_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_3_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_3_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_4_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_4_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_4_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_4_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_4_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_5_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_5_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_5_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_5_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_5_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_6_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_6_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_6_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_6_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_6_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_7_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_7_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_7_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_7_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_7_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_8_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_8_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_8_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_8_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_8_R1.fastp_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.fastp_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_9_R1.fastp_bismark_bt2_PE_report.txt < Processing alignment report zr3644_9_R1.fastp_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_9_R1.fastp_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_9_R1.fastp_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_9_R1.fastp_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 46 Bismark BAM file(s)... >> Reading from Bismark report: 0501_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 0502_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 0503_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 3501_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 3502_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 3503_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5201_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5202_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5203_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5901_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5902_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5903_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_10_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_1_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_2_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_3_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_4_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_5_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_6_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_7_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_8_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_9_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_10_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_11_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_12_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_13_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_14_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_15_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_16_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_17_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_18_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_19_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_1_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_20_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_21_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_22_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_23_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_24_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_2_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_3_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_4_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_5_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_6_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_7_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_8_R1.fastp_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_9_R1.fastp_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/sr320/060821-bigC [INFO ] bismark : Found 46 bismark alignment reports [INFO ] bismark : Found 46 bismark dedup reports [INFO ] bismark : Found 46 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... [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... [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... Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 0501_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 0501_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 96 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 20736 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 23153 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 21645 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 17711 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 21389 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 22344 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 22564 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 19728 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 13819 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 20380 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 272 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 341 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 214 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 183 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 188 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 185 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 173 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 157 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 433 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 133 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 207 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 189 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 342 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 172 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 192 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 168 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 167 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 796 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 224 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 188 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 226 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 199 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 162 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 160 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 190 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 280 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 95 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 19 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 229 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994914.1 Writing cytosine report for not covered chromosome NW_022994930.1 Writing cytosine report for not covered chromosome NW_022994953.1 Writing cytosine report for not covered chromosome NW_022994976.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>0501_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 0501_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 0502_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 0502_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 72 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 22028 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 21652 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 22370 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 17564 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 21445 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 23607 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 22160 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 19783 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 13922 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 20343 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 241 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 270 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 199 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 212 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 170 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 179 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 443 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 171 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 234 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 237 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 177 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 214 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 262 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 720 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 195 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 192 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 160 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 193 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 200 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 190 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 162 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 317 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 280 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 198 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 210 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 91 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 8 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 229 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994875.1 Writing cytosine report for not covered chromosome NW_022994912.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994976.1 Writing cytosine report for not covered chromosome NW_022994980.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>0502_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 0502_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 0503_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 0503_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 56 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 20720 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 22406 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 21438 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 16718 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 21310 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 21766 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 22334 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 19096 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 13283 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 20019 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 201 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 135 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 181 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 162 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 216 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 237 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 135 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 251 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 164 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 189 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 294 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 192 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 188 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 232 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 168 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 237 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 669 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 340 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 226 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 170 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 223 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 208 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 302 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 188 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 217 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 157 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 218 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 127 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 10 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 229 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994779.1 Writing cytosine report for not covered chromosome NW_022994796.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994874.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>0503_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 0503_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 3501_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 3501_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 85 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 21339 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 21761 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 22200 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 18533 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 21855 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 21823 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 22511 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 18883 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 13464 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 20487 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 317 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 169 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 194 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 188 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 165 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 217 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 185 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 324 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 153 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 162 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 204 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 216 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 235 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 135 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 244 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 743 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 181 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 163 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 190 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 210 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 271 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 255 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 278 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 100 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 18 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 230 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994981.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>3501_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 3501_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 3502_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 3502_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 115 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 21845 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 22676 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 22132 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 18201 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 21515 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 22940 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 23804 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 19852 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 14083 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 21372 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 265 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 309 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 199 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 267 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 193 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 190 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 169 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 164 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 442 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 247 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 243 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 261 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 256 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 825 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 240 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 242 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 172 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 169 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 307 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 279 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 155 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 188 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 203 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 146 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 177 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 94 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 16 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 230 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994803.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>3502_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 3502_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 3503_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 3503_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 120 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 20437 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 22504 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 21211 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 17847 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 21831 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 21993 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 22214 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 18887 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 13154 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 20357 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 210 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 221 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 210 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 209 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 190 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 371 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 210 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 223 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 251 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 233 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 301 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 214 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 670 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 193 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 193 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 205 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 159 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 185 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 135 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 163 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 323 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 223 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 174 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 183 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 169 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 92 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 14 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 231 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994898.1 Writing cytosine report for not covered chromosome NW_022994984.1 Writing cytosine report for not covered chromosome NW_022994988.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>3503_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 3503_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 5201_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 5201_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 120 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 19947 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 19969 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 20733 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 16329 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 19391 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 20047 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 21060 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 17976 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 11885 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 18771 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 196 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 241 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 190 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 237 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 312 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 133 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 249 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 248 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 163 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 181 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 669 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 182 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 219 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 160 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 197 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 224 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 75 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 28 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 226 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994798.1 Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994908.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994942.1 Writing cytosine report for not covered chromosome NW_022994953.1 Writing cytosine report for not covered chromosome NW_022994981.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>5201_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 5201_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 5202_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 5202_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 157 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 21699 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 23941 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 23400 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 19153 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 22838 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 24856 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 24289 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 21944 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 14013 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 21687 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 212 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 269 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 240 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 183 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 253 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 168 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 234 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 288 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 441 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 170 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 198 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 232 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 298 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 501 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 258 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 779 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 432 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 225 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 190 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 162 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 135 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 382 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 350 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 186 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 195 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 175 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 276 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 57 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 41 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 230 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994907.1 Writing cytosine report for not covered chromosome NW_022994933.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>5202_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 5202_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 5203_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 5203_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 132 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 20793 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 22787 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 21088 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 17674 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 19715 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 20996 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 21494 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 19183 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 13243 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 19999 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 251 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 270 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 189 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 234 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 274 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 386 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 200 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 169 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 172 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 192 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 400 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 273 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 646 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 207 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 222 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 150 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 170 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 255 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 226 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 188 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 153 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 101 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 7 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 231 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>5203_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 5203_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 5901_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 5901_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 87 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 22113 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 21868 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 23604 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 18150 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 21891 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 22970 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 23981 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 20129 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 13912 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 22657 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 209 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 364 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 197 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 170 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 185 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 349 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 277 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 157 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 266 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 146 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 394 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 196 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 553 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 218 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 198 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 211 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 170 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 192 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 294 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 207 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 157 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 177 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 88 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 10 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 231 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994912.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994981.1 Writing cytosine report for not covered chromosome NW_022994990.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>5901_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 5901_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 5902_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 5902_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 146 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 23202 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 21248 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 23081 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 19505 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 23216 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 24728 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 24577 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 20699 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 13700 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 22548 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 269 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 181 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 302 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 194 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 192 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 460 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 168 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 133 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 258 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 214 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 163 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 361 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 243 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 798 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 216 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 218 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 165 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 193 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 213 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 160 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 278 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 314 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 223 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 207 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 160 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 87 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 21 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 225 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994796.1 Writing cytosine report for not covered chromosome NW_022994798.1 Writing cytosine report for not covered chromosome NW_022994802.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994912.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Writing cytosine report for not covered chromosome NW_022994988.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>5902_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 5902_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 5903_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: 5903_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 168 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 23534 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 23658 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 24224 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 19905 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 23258 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 23969 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 24487 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 20607 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 14598 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 22846 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 215 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 310 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 158 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 170 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 198 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 285 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 203 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 199 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 177 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 454 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 135 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 373 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 235 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 377 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 187 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 720 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 296 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 210 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 248 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 277 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 330 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 293 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 198 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 264 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 125 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 26 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 233 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994795.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>5903_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 5903_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_10_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_10_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 128 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17334 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15702 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17262 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13972 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 14689 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18113 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18905 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14510 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10693 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17225 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 135 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 279 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 204 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 245 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 155 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 167 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 444 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 168 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 166 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 59 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 4 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 227 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994803.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994888.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994942.1 Writing cytosine report for not covered chromosome NW_022994953.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_10_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_10_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_1_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_1_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 57 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 16965 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 14427 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17717 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14404 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15796 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18368 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18316 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 15041 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 9718 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16778 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 174 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 199 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 193 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 153 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 160 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 602 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 157 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 236 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 79 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 12 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 226 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994796.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994803.1 Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994827.1 Writing cytosine report for not covered chromosome NW_022994971.1 Writing cytosine report for not covered chromosome NW_022994980.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_1_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_1_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_2_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_2_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 89 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17157 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 14878 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17597 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13414 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 16081 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18035 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18665 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14395 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10461 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16645 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 182 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 261 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 280 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 194 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 203 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 354 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 210 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 182 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 146 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 174 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 81 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 13 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 226 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994905.1 Writing cytosine report for not covered chromosome NW_022994947.1 Writing cytosine report for not covered chromosome NW_022994953.1 Writing cytosine report for not covered chromosome NW_022994981.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_2_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_2_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_3_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_3_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 44 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17101 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 14859 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 18540 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13400 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15878 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18184 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18229 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14363 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10103 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17246 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 164 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 190 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 234 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 184 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 209 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 227 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 405 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 232 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 165 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 126 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 16 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 227 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994787.1 Writing cytosine report for not covered chromosome NW_022994788.1 Writing cytosine report for not covered chromosome NW_022994795.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994908.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_3_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_3_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_4_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_4_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 80 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17078 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15052 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17142 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13809 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 16009 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18086 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 17847 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14176 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10688 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16854 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 194 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 190 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 263 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 133 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 169 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 453 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 160 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 183 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 249 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 186 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 80 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 17 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 226 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994781.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994930.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994980.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_4_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_4_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_5_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_5_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 98 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 16887 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15358 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17010 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13912 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15104 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 17140 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 17245 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14015 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 9971 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16681 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 231 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 292 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 189 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 289 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 159 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 625 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 213 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 259 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 200 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 85 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 10 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 225 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994929.1 Writing cytosine report for not covered chromosome NW_022994931.1 Writing cytosine report for not covered chromosome NW_022994947.1 Writing cytosine report for not covered chromosome NW_022994953.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_5_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_5_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_6_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_6_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 75 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 16427 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15024 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 16804 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13477 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15121 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 17941 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 17950 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 13763 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10791 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16728 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 217 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 210 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 166 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 447 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 169 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 168 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 159 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 186 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 80 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 2 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 220 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994795.1 Writing cytosine report for not covered chromosome NW_022994804.1 Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994884.1 Writing cytosine report for not covered chromosome NW_022994912.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994929.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994953.1 Writing cytosine report for not covered chromosome NW_022994976.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994981.1 Writing cytosine report for not covered chromosome NW_022994984.1 Writing cytosine report for not covered chromosome NW_022994994.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_6_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_6_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_7_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_7_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 85 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 16634 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15590 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17494 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13834 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15091 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18325 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18238 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14396 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10728 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16640 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 181 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 209 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 187 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 155 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 202 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 422 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 155 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 260 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 174 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 150 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 90 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 16 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 222 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994776.1 Writing cytosine report for not covered chromosome NW_022994790.1 Writing cytosine report for not covered chromosome NW_022994795.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994884.1 Writing cytosine report for not covered chromosome NW_022994898.1 Writing cytosine report for not covered chromosome NW_022994908.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994976.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_7_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_7_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_8_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_8_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 86 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 16189 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 14450 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 16826 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13204 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15281 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 16731 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 17632 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 13580 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10977 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 15658 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 243 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 159 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 254 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 194 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 174 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 386 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 133 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 92 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 15 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 222 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994788.1 Writing cytosine report for not covered chromosome NW_022994791.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994883.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994953.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994988.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_8_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_8_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_9_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_9_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 60 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17440 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15840 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 18127 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13829 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15827 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 17926 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18056 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14828 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10661 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17163 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 146 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 202 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 218 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 166 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 214 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 165 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 191 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 166 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 378 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 167 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 263 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 190 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 46 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 9 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 230 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994907.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_9_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_9_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_10_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_10_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 178 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17066 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15550 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17856 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13762 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15438 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18292 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18287 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14777 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10582 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17268 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 153 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 206 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 269 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 174 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 397 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 203 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 174 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 183 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 167 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 93 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 22 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 228 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994930.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994981.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_10_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_10_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_11_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_11_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 145 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 16867 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 14933 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17182 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13986 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15942 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18128 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18184 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14488 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10884 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16776 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 278 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 166 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 213 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 158 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 199 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 422 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 150 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 209 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 185 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 90 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 6 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 227 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994780.1 Writing cytosine report for not covered chromosome NW_022994796.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994914.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994976.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_11_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_11_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_12_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_12_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 168 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17205 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15410 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17520 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13551 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15250 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 17650 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18035 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14341 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 9805 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16632 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 146 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 172 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 347 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 155 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 268 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 217 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 146 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 76 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 8 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 227 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994790.1 Writing cytosine report for not covered chromosome NW_022994795.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_12_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_12_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_13_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_13_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 264 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17088 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15827 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17703 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13892 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15936 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18543 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18388 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14807 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 11168 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17417 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 310 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 205 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 267 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 202 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 167 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 184 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 183 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 478 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 179 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 229 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 236 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 159 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 188 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 78 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 7 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 223 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994790.1 Writing cytosine report for not covered chromosome NW_022994796.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994801.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994898.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994947.1 Writing cytosine report for not covered chromosome NW_022994971.1 Writing cytosine report for not covered chromosome NW_022994976.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994981.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_13_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_13_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_14_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_14_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 183 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17149 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 16037 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17882 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14158 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15452 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18326 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18761 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14764 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10627 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17395 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 239 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 284 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 181 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 195 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 196 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 240 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 133 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 555 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 181 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 201 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 253 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 114 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 6 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 224 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994788.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994853.1 Writing cytosine report for not covered chromosome NW_022994871.1 Writing cytosine report for not covered chromosome NW_022994898.1 Writing cytosine report for not covered chromosome NW_022994905.1 Writing cytosine report for not covered chromosome NW_022994908.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994953.1 Writing cytosine report for not covered chromosome NW_022994980.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_14_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_14_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_15_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_15_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 319 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17372 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15210 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17702 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14813 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15771 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18183 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18559 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 15103 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10636 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16793 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 250 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 185 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 153 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 219 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 177 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 372 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 157 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 225 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 193 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 179 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 71 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 9 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 224 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994773.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994884.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994942.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_15_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_15_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_16_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_16_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 285 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 16794 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 13913 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 16711 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13601 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 14917 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 17586 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 17636 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 13600 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10775 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16396 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 276 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 226 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 183 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 201 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 208 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 233 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 206 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 430 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 175 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 146 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 236 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 164 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 157 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 105 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 3 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 229 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994980.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_16_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_16_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_17_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_17_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 354 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17281 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15417 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17121 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14157 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15634 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18063 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18202 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14094 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10527 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16744 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 317 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 146 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 196 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 185 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 298 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 231 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 218 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 236 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 479 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 167 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 135 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 165 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 194 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 225 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 200 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 70 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 18 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 229 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994803.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994854.1 Writing cytosine report for not covered chromosome NW_022994898.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_17_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_17_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_18_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_18_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 342 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17325 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15231 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17741 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14405 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15318 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18906 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 19198 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 15233 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10907 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17596 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 230 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 206 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 157 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 234 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 191 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 437 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 165 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 242 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 171 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 48 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 12 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 232 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994953.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_18_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_18_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_19_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_19_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 158 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17492 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15524 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17779 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14761 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15369 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18545 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18530 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14764 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10745 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17433 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 287 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 178 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 254 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 185 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 155 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 236 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 517 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 175 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 209 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 214 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 85 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 223 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994788.1 Writing cytosine report for not covered chromosome NW_022994795.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994971.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Writing cytosine report for not covered chromosome NW_022994994.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_19_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_19_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_1_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_1_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 254 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 16693 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15519 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17303 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13344 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15170 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 17985 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18448 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14841 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10264 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16712 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 205 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 167 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 259 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 204 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 233 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 183 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 208 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 470 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 165 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 191 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 201 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 93 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 32 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 230 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_1_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_1_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_20_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_20_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 340 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17325 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 16151 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17705 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14257 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15981 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18420 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 19604 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14956 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10475 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 18123 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 169 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 236 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 185 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 172 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 211 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 168 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 185 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 449 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 133 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 177 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 223 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 99 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 15 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 227 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994781.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994930.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Writing cytosine report for not covered chromosome NW_022994994.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_20_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_20_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_21_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_21_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 214 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17184 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15898 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 18282 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14477 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15453 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18142 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 19210 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14718 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10985 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17663 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 235 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 176 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 225 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 227 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 175 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 497 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 159 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 217 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 270 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 116 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 23 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 227 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994798.1 Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994912.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994942.1 Writing cytosine report for not covered chromosome NW_022994950.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_21_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_21_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_22_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_22_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 318 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17100 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15282 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 18468 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14874 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15595 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18906 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18306 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 15168 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10847 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17240 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 247 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 232 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 199 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 158 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 168 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 309 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 230 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 213 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 150 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 189 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 85 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 10 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 228 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994776.1 Writing cytosine report for not covered chromosome NW_022994788.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994950.1 Writing cytosine report for not covered chromosome NW_022994976.1 Writing cytosine report for not covered chromosome NW_022994992.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_22_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_22_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_23_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_23_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 224 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 16988 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15351 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17838 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13251 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15751 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18306 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 17691 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14613 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10310 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17302 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 223 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 252 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 196 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 182 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 375 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 142 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 197 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 186 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 170 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 90 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 11 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 227 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994802.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994914.1 Writing cytosine report for not covered chromosome NW_022994942.1 Writing cytosine report for not covered chromosome NW_022994970.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_23_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_23_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_24_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_24_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 243 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17767 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15339 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 18336 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14169 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 16093 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18447 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 19189 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 15307 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 11181 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17728 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 217 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 210 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 200 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 231 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 261 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 460 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 177 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 182 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 260 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 133 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 161 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 135 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 105 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 3 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 227 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994788.1 Writing cytosine report for not covered chromosome NW_022994790.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994898.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_24_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_24_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_2_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_2_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 215 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17027 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 14726 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17581 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13910 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15141 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18270 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18479 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14027 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 14243 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16653 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 231 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 276 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 146 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 141 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 343 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 197 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 207 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 233 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 172 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 472 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 159 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 164 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 255 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 263 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 148 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 127 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 4 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 227 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994795.1 Writing cytosine report for not covered chromosome NW_022994798.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994914.1 Writing cytosine report for not covered chromosome NW_022994930.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_2_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_2_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_3_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_3_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 227 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17085 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 16174 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17628 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13889 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15961 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18218 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18168 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14127 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 11512 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16781 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 159 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 260 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 179 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 229 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 223 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 279 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 283 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 153 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 419 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 184 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 213 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 193 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 133 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 67 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 17 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 226 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994803.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994906.1 Writing cytosine report for not covered chromosome NW_022994913.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994950.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_3_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_3_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_4_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_4_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 236 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 16686 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15484 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17697 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14196 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15510 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 17561 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 17901 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14734 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10035 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16876 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 238 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 159 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 126 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 151 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 124 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 231 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 165 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 178 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 482 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 164 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 167 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 205 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 230 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 75 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 10 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 228 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994779.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994808.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994984.1 Writing cytosine report for not covered chromosome NW_022994988.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_4_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_4_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_5_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_5_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 287 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17563 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15187 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 18017 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14591 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15620 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18719 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18379 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14386 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10805 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 17299 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 187 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 248 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 136 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 198 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 133 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 134 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 233 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 139 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 452 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 129 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 140 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 249 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 222 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 155 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 128 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 114 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 85 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 10 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 230 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994898.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_5_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_5_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_6_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_6_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 210 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17500 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15820 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17826 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14341 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15755 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18542 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18827 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14877 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10643 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16953 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 193 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 150 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 164 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 122 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 180 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 230 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 99 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 162 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 229 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 174 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 448 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 115 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 143 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 203 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 280 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 177 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 156 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 81 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 16 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 224 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994788.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994912.1 Writing cytosine report for not covered chromosome NW_022994914.1 Writing cytosine report for not covered chromosome NW_022994926.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994942.1 Writing cytosine report for not covered chromosome NW_022994950.1 Writing cytosine report for not covered chromosome NW_022994980.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_6_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_6_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_7_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_7_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 278 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17089 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15926 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17795 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 14102 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15051 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18708 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 18742 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14307 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10872 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16922 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 137 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 121 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 239 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 208 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 214 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 152 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 525 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 89 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 138 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 159 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 169 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 77 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 66 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 227 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 200 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 118 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 88 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 70 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 112 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 20 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 227 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994779.1 Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994884.1 Writing cytosine report for not covered chromosome NW_022994909.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994942.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_7_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_7_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_8_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_8_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 258 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 17353 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 15319 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 17859 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13826 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 15978 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 18765 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 17781 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 14609 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10525 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16859 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 95 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 205 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 104 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 101 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 90 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 164 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 244 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 73 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 168 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 100 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 260 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 75 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 169 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 463 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 54 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 131 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 135 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 83 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 130 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 120 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 43 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 125 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 232 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 162 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 72 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 149 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 123 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 74 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 41 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 93 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 14 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 61 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 70 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 20 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 225 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994797.1 Writing cytosine report for not covered chromosome NW_022994802.1 Writing cytosine report for not covered chromosome NW_022994807.1 Writing cytosine report for not covered chromosome NW_022994811.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994817.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994914.1 Writing cytosine report for not covered chromosome NW_022994941.1 Writing cytosine report for not covered chromosome NW_022994953.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_8_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_8_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3644_9_R1.fastp_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/060821-bigC/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no 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) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3644_9_R1.fastp.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 246 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 15979 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 14288 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 16206 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 13534 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 14891 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 17014 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 17314 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 13598 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 10181 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 16531 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 147 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 117 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 154 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 17 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 106 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 68 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 69 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 52 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 44 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 240 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 85 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 56 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 57 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 82 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 24 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 62 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 80 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 46 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 59 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 127 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 182 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 94 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 168 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 38 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 65 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 25 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 96 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 443 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 145 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 28 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 103 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 45 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 30 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 8 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 33 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 81 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 84 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 49 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 11 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 19 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 9 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 92 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 102 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 36 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 31 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 6 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 13 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 63 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 119 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 76 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 78 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 51 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 79 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 260 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 97 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 167 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 47 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 87 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 71 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 12 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 105 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 98 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 34 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 42 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 16 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 58 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 48 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 64 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 39 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 37 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 146 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 23 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 20 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 91 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 18 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 60 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 26 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 29 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 21 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 27 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 53 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 40 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 5 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 15 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 55 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 32 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 67 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 7 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 86 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 50 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 35 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 22 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 10 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 92 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 7 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 228 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994779.1 Writing cytosine report for not covered chromosome NW_022994795.1 Writing cytosine report for not covered chromosome NW_022994812.1 Writing cytosine report for not covered chromosome NW_022994814.1 Writing cytosine report for not covered chromosome NW_022994818.1 Writing cytosine report for not covered chromosome NW_022994905.1 Writing cytosine report for not covered chromosome NW_022994942.1 Writing cytosine report for not covered chromosome NW_022994971.1 Writing cytosine report for not covered chromosome NW_022994984.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3644_9_R1.fastp.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3644_9_R1.fastp.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq!