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) 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-big'): /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-big 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 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 (65141953 sequences in total) 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 (65141953 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 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1115:10399:36768_1:N:0:CGATGT NW_022994924.1 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1120:3295:11277_1:N:0:CGATGT NW_022994968.1 91866 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1121:20506:49812_1:N:0:CGATGT NW_022994966.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1124:17401:24567_1:N:0:CGATGT NW_022994968.1 91868 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1202:28970:39018_1:N:0:CGATGT NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1203:12773:36979_1:N:0:CGATGT NW_022994963.1 286836 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1207:10429:50006_1:N:0:CGATGT NC_001276.1 18087 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1208:18010:71506_1:N:0:CGATGT NW_022994893.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1210:4137:56018_1:N:0:CGATGT NC_001276.1 18094 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1212:29894:15865_1:N:0:CGATGT NW_022994881.1 520507 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1212:6573:44134_1:N:0:CGATGT NW_022994881.1 520503 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1213:10439:57723_1:N:0:CGATGT NW_022994810.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1214:18406:69660_1:N:0:CGATGT NW_022994814.1 2 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1215:27011:36750_1:N:0:CGATGT NW_022994936.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1216:23054:62980_1:N:0:CGATGT NC_001276.1 3 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1217:17969:66830_1:N:0:CGATGT NW_022994972.1 189610 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1218:21572:66425_1:N:0:CGATGT NC_001276.1 1 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1224:11383:45365_1:N:0:CGATGT NW_022994936.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1224:21014:51500_1:N:0:CGATGT NC_001276.1 18101 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2103:17026:2258_1:N:0:CGATGT NW_022994975.1 74043 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2105:3924:50832_1:N:0:CGATGT NC_001276.1 18089 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2105:18142:69238_1:N:0:CGATGT NW_022994929.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2106:5893:45734_1:N:0:CGATGT NW_022994912.1 2 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2110:13179:52871_1:N:0:CGATGT NC_001276.1 18097 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2110:7963:71154_1:N:0:CGATGT NW_022994804.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2110:8085:71154_1:N:0:CGATGT NW_022994804.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2112:15351:28330_1:N:0:CGATGT NC_001276.1 1 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2114:7567:58409_1:N:0:CGATGT NW_022994905.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2115:2595:46701_1:N:0:CGATGT NC_001276.1 1 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2203:20060:64439_1:N:0:CGATGT NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2204:11779:27169_1:N:0:CGATGT NW_022994974.1 36458 Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2210:20314:66039_1:N:0:CGATGT NW_022994902.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2211:4838:19961_1:N:0:CGATGT NW_022994893.1 1 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2221:5081:39827_1:N:0:CGATGT NW_022994888.1 1 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2222:27641:20049_1:N:0:CGATGT NW_022994814.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2222:8085:57301_1:N:0:CGATGT NW_022994814.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2223:27762:47263_1:N:0:CGATGT NW_022994931.1 118200 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2224:20172:48459_1:N:0:CGATGT NW_022994824.1 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1101:8247:59938_1:N:0:CGATGT NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1102:24576:59921_1:N:0:CGATGT NW_022994803.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1102:10541:66443_1:N:0:CGATGT NW_022994946.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1104:19837:16164_1:N:0:CGATGT NC_001276.1 1 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1105:5365:23302_1:N:0:CGATGT NC_001276.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1107:26342:54541_1:N:0:CGATGT NW_022994946.1 2 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1108:14905:32056_1:N:0:CGATGT NW_022994881.1 520507 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1108:13859:73000_1:N:0:CGATGT NW_022994909.1 80202 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1110:30218:39141_1:N:0:CGATGT NC_001276.1 1 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1112:12266:60501_1:N:0:CGATGT NW_022994900.1 158467 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1116:18314:52238_1:N:0:CGATGT NC_001276.1 1 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1119:10957:3559_1:N:0:CGATGT NW_022994777.1 1 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1123:21247:47193_1:N:0:CGATGT NW_022994810.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1123:13606:59868_1:N:0:CGATGT NC_001276.1 2 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1202:23145:25728_1:N:0:CGATGT NW_022994939.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1203:12347:34940_1:N:0:CGATGT NW_022994936.1 296905 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1205:27671:64615_1:N:0:CGATGT NC_001276.1 1 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1208:19187:6495_1:N:0:CGATGT NW_022994792.1 66653 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1209:13514:52678_1:N:0:CGATGT NW_022994970.1 1 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1212:3752:30984_1:N:0:CGATGT NC_001276.1 18095 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1212:22577:52520_1:N:0:CGATGT NC_001276.1 18084 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1214:4817:10328_1:N:0:CGATGT NC_001276.1 18101 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1215:21501:9202_1:N:0:CGATGT NW_022994936.1 1 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1215:24566:30439_1:N:0:CGATGT NW_022994968.1 91857 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1217:10947:61591_1:N:0:CGATGT NW_022994975.1 74046 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1221:13961:61890_1:N:0:CGATGT NW_022994929.1 2 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1222:6492:35203_1:N:0:CGATGT NW_022994940.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2101:10967:24075_1:N:0:CGATGT NW_022994810.1 1 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2103:3204:47509_1:N:0:CGATGT NW_022994956.1 433803 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2105:5416:54752_1:N:0:CGATGT NW_022994998.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2105:19745:60976_1:N:0:CGATGT NW_022994881.1 520524 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2106:9942:21983_1:N:0:CGATGT NW_022994957.1 201017 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2106:7841:66759_1:N:0:CGATGT NW_022994989.1 2 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2108:8572:67392_1:N:0:CAATGT NW_022994810.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2109:27407:33674_1:N:0:CGATGT NW_022994968.1 91862 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2116:23734:69010_1:N:0:CGATGT NW_022994778.1 761844 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2117:4411:14406_1:N:0:CGATGT NW_022994893.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2117:13829:36733_1:N:0:CGATGT NW_022994810.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2119:23297:5915_1:N:0:CGATGT NC_001276.1 2 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2120:23652:10609_1:N:0:CGATGT NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2120:13474:11576_1:N:0:CGATGT NW_022994975.1 74046 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2120:26250:45452_1:N:0:CGATGT NW_022994893.1 1 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2124:12428:72104_1:N:0:CGATGT NW_022994931.1 118203 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2206:25631:64949_1:N:0:CGATGT NW_022994814.1 2 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2211:26788:31933_1:N:0:CGATGT NW_022994963.1 286836 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2214:2991:7093_1:N:0:CGATGT NW_022994994.1 3 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2217:20029:21948_1:N:0:CGATGT NC_001276.1 1 Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2218:10226:69062_1:N:0:CGATGT NW_022994970.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2219:15067:13000_1:N:0:CGATGT NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2219:15057:13123_1:N:0:CGATGT NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2220:21197:24075_1:N:0:CGATGT NW_022994817.1 2130 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2221:5122:19469_1:N:0:CGATGT NW_022994917.1 38987 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2221:12743:69730_1:N:0:CGATGT NW_022994924.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2223:28716:29964_1:N:0:CGATGT NW_022994968.1 91862 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2223:2412:72016_1:N:0:CGATGT NW_022994963.1 286824 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1144:25608:6073_1:N:0:CGATGT NW_022994963.1 286836 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1240:28546:2018_1:N:0:CGATGT NW_022994915.1 2 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1245:19696:8985_1:N:0:CGATGT NW_022994970.1 1 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1265:26359:11819_1:N:0:CGATGT NW_022994978.1 2 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1277:10800:18881_1:N:0:CGATGT NW_022994972.1 1 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1304:27959:34287_1:N:0:CGATGT NW_022994968.1 91883 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1315:4643:3270_1:N:0:CGATGT NW_022994966.1 1 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1319:20455:25864_1:N:0:CGATGT NW_022994955.1 365335 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1346:31982:6684_1:N:0:CGATGT NW_022994966.1 1 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1426:23086:27258_1:N:0:CGATGT NW_022994965.1 30548 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1452:13395:36025_1:N:0:CGATGT NC_001276.1 1 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1452:13413:36025_1:N:0:CGATGT NC_001276.1 1 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1461:27597:32503_1:N:0:CGATGT NW_022994974.1 36463 Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1622:18873:34397_1:N:0:CGATGT NW_022994893.1 1 Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2307:24388:3051_1:N:0:CGATGT NC_001276.1 18100 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2362:12066:18881_1:N:0:CGATGT NW_022994968.1 91883 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2442:27877:27539_1:N:0:CGATGT NW_022994929.1 1 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2528:22535:3129_1:N:0:CGATGT NW_022994948.1 858047 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2648:28546:6778_1:N:0:CGATGT NW_022994940.1 1 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2652:26946:3317_1:N:0:CGATGT NW_022994921.1 323389 Processed 65000000 sequence pairs so far 65141953 reads; of these: 65141953 (100.00%) were paired; of these: 35559597 (54.59%) aligned concordantly 0 times 13966181 (21.44%) aligned concordantly exactly 1 time 15616175 (23.97%) aligned concordantly >1 times 45.41% overall alignment rate 65141953 reads; of these: 65141953 (100.00%) were paired; of these: 64887900 (99.6165141953%65141953 reads; of these:) aligned concordantly 0 times reads; of these: 6514195315521665141953 ( ( (0.24%) aligned concordantly exactly 1 time 100.00 100.00%98837%) were paired; of these: () were paired; of these: 0.15 % 35579697) aligned concordantly >1 times64885801 ( (54.620.3999.61%%%) aligned concordantly 0 times overall alignment rate) aligned concordantly 0 times 13961962 ( 21.43158467% () aligned concordantly exactly 1 time0.24 % ) aligned concordantly exactly 1 time15600294 ( 23.9597685% () aligned concordantly >1 times0.15 %45.38) aligned concordantly >1 times% overall alignment rate0.39 % overall alignment rate Processed 65141953 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: 65141953 Number of paired-end alignments with a unique best hit: 37645135 Mapping efficiency: 57.8% Sequence pairs with no alignments under any condition: 20942583 Sequence pairs did not map uniquely: 6554235 Sequence pairs which were discarded because genomic sequence could not be extracted: 113 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 18822737 ((converted) top strand) GA/CT/CT: 9297 (complementary to (converted) top strand) GA/CT/GA: 9785 (complementary to (converted) bottom strand) CT/GA/GA: 18803203 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1584302702 Total methylated C's in CpG context: 25793251 Total methylated C's in CHG context: 2432311 Total methylated C's in CHH context: 11122417 Total methylated C's in Unknown context: 187601 Total unmethylated C's in CpG context: 165055619 Total unmethylated C's in CHG context: 257497707 Total unmethylated C's in CHH context: 1122401397 Total unmethylated C's in Unknown context: 4764641 C methylated in CpG context: 13.5% C methylated in CHG context: 0.9% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.8% Bismark completed in 0d 6h 53m 6s ==================== 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) 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-big'): /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-big 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 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 (58618241 sequences in total) 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 (58618241 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 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1102:22719:64615_1:N:0:CAGATC NW_022994893.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1104:19299:31511_1:N:0:CAGATC NC_001276.1 18096 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1108:7436:56071_1:N:0:CAGATC NW_022994950.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1109:16244:12507_1:N:0:CAGATC NW_022994810.1 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1112:14235:6812_1:N:0:CAGATC NW_022994935.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1113:4371:36733_1:N:0:CAGATC NW_022994940.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1114:8217:4122_1:N:0:CAGATC NW_022994810.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1114:6512:13510_1:N:0:CAGATC NW_022994921.1 323392 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1114:21978:39669_1:N:0:CAGATC NW_022994936.1 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1116:9262:23231_1:N:0:CAGATC NW_022994989.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1117:25367:32320_1:N:0:CAGATC NC_001276.1 18106 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1117:23713:54805_1:N:0:CAGATC NW_022994921.1 323386 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1123:5528:3964_1:N:0:CAGATC NW_022994939.1 324514 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1123:5112:4227_1:N:0:CAGATC NW_022994939.1 324514 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1124:4635:15285_1:N:0:CAGATC NW_022994970.1 36291 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1202:17523:40108_1:N:0:CAGATC NW_022994916.1 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1203:3478:13035_1:N:0:CAGATC NW_022994844.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1203:26565:24233_1:N:0:CAGATC NW_022994940.1 2 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1206:3762:45734_1:N:0:CAGATC NC_001276.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1209:21978:43853_1:N:0:CAGATC NC_001276.1 2 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1210:28655:64316_1:N:0:CAGATC NW_022994806.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1211:25388:53451_1:N:0:CAGATC NC_001276.1 18097 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1211:11688:61784_1:N:0:CAGATC NW_022994972.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1212:24799:26554_1:N:0:CAGATC NW_022994918.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1212:24048:61784_1:N:0:CAGATC NW_022994968.1 91861 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1213:17442:5194_1:N:0:CAGATC NC_001276.1 1 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1214:4574:51887_1:N:0:CAGATC NW_022994970.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1215:24789:44433_1:N:0:CAGATC NW_022994916.1 77660 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1215:17188:73211_1:N:0:CAGATC NC_001276.1 1 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1219:9404:57829_1:N:0:CAGATC NW_022994940.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1221:6086:39106_1:N:0:CAGATC NW_022994940.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1221:6076:39264_1:N:0:CAGATC NW_022994940.1 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1221:14976:65933_1:N:0:CAGATC NC_001276.1 18088 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1222:20425:44714_1:N:0:CAGATC NW_022994935.1 43666 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1224:8278:64245_1:N:0:CAGATC NW_022994939.1 1 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2102:24495:41602_1:N:0:CAGATC NW_022994786.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2102:29427:59569_1:N:0:CAGATA NW_022994930.1 1 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2106:17198:30052_1:N:0:CAGATC NW_022994985.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2108:11211:27029_1:N:0:CAGATC NW_022994936.1 296902 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2108:2351:55948_1:N:0:CAGATC NC_001276.1 1 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2110:19664:32988_1:N:0:CAGATC NW_022994827.1 1 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2114:20750:44679_1:N:0:CAGATC NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2114:7517:59868_1:N:0:CAGATC NW_022994893.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2115:13068:1942_1:N:0:CAGATC NW_022994810.1 2 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2117:8958:45593_1:N:0:CAGATC NW_022994957.1 201007 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2117:22810:72719_1:N:0:CAGATC NW_022994896.1 1 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2121:8420:41743_1:N:0:CAGATC NW_022994968.1 91867 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2122:30878:14230_1:N:0:CAGATC NW_022994909.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2122:30949:14248_1:N:0:CAGATC NW_022994909.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2122:19076:69062_1:N:0:CAGATC NW_022994966.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2123:30269:53153_1:N:0:CAGATC NW_022994965.1 1 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2204:22769:29929_1:N:0:CAGATC NW_022994810.1 2 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2212:20131:7568_1:N:0:CAGATC NW_022994946.1 333508 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2212:22221:55842_1:N:0:CAGATC NC_001276.1 18094 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2218:30807:43044_1:N:0:CAGATC NW_022994817.1 2119 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2219:27559:62945_1:N:0:CAGATC NW_022994971.1 30248 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2220:5365:21895_1:N:0:CAGATC NW_022994968.1 91861 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2220:23987:55561_1:N:0:CAGATC NW_022994919.1 196096 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2224:30025:23372_1:N:0:CAGATC NW_022994905.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2224:30249:23407_1:N:0:CAGATC NW_022994905.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1102:28138:63279_1:N:0:CAGATC NW_022994947.1 135648 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1106:17837:13228_1:N:0:CAGATC NW_022994902.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1106:18944:34693_1:N:0:CAGATC NW_022994912.1 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1107:6999:62628_1:N:0:CAGATC NW_022994939.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1110:19147:2768_1:N:0:CAGATC NW_022994975.1 74063 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1110:27438:52010_1:N:0:CAGATC NW_022994956.1 433816 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1117:26220:6618_1:N:0:CAGATC NW_022994969.1 256193 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1117:18588:71805_1:N:0:CAGATC NW_022994936.1 2 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1119:10064:20788_1:N:0:CAGATC NW_022994810.1 1 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1122:7912:35168_1:N:0:CAGATC NW_022994881.1 520503 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1122:13707:53645_1:N:0:CAGATC NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1124:4696:69889_1:N:0:CAGATC NW_022994931.1 118183 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1202:7963:58778_1:N:0:CAGATC NC_001276.1 1 Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1210:29041:24093_1:N:0:CAGATC NW_022994919.1 196109 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1210:25865:57372_1:N:0:CAGATC NW_022994814.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1210:9729:66584_1:N:0:CAGATC NC_001276.1 1 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1213:26930:48353_1:N:0:CAGATC NC_001276.1 1 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1216:19116:46455_1:N:0:CAGATC NW_022994928.1 69251 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1216:9973:71858_1:N:0:CAGATC NC_001276.1 18101 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1218:6248:3735_1:N:0:CAGATC NW_022994946.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1218:16062:31388_1:N:0:CAGATC NC_001276.1 18098 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1218:8126:50058_1:N:0:CAGATC NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1218:8156:50076_1:N:0:CAGATC NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1219:27955:47527_1:N:0:CAGATC NW_022994803.1 2 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1220:23054:60659_1:N:0:CAGATC NW_022994975.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1220:22800:60712_1:N:0:CAGATC NW_022994975.1 1 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1223:22019:52397_1:N:0:CAGATC NW_022994966.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:1224:21146:53100_1:N:0:CAGATC NW_022994974.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2101:21237:12718_1:N:0:CAGATC NW_022994786.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2101:16366:14090_1:N:0:CAGATC NW_022994944.1 261194 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2106:26798:5546_1:N:0:CAGATC NW_022994972.1 189615 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2106:6654:58620_1:N:0:CAGATC NW_022994968.1 91865 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2108:18822:29033_1:N:0:CAGATC NW_022994931.1 118205 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2114:23632:50515_1:N:0:CAGATC NC_001276.1 1 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2115:12023:35326_1:N:0:CAGATC NW_022994940.1 1 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2119:5812:27521_1:N:0:CAGATC NW_022994985.1 189966 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2119:5720:27574_1:N:0:CAGATC NW_022994985.1 189966 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2120:22333:7796_1:N:0:CAGATC NW_022994966.1 1 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2201:2027:69344_1:N:0:CAGATC NC_001276.1 2 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2206:27752:1819_1:N:0:CAGATC NW_022994950.1 1 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2207:10247:14740_1:N:0:CAGATC NW_022994893.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2207:6451:45048_1:N:0:CAGATC NW_022994958.1 1 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2212:13930:7550_1:N:0:CAGATC NW_022994810.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2214:20446:8851_1:N:0:CAGATC NW_022994933.1 29852 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2217:12033:3419_1:N:0:CAGATC NC_001276.1 18085 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2218:9587:55790_1:N:0:CAGATC NW_022994951.1 187603 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2218:9232:56229_1:N:0:CAGATC NW_022994951.1 187603 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2219:7831:7919_1:N:0:CAGATC NW_022994985.1 189971 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:7:2223:18659:28259_1:N:0:CAGATC NW_022994972.1 189609 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1451:31810:17190_1:N:0:CAGATC NW_022994975.1 2 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1502:24135:4993_1:N:0:CAGATC NW_022994971.1 1 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1514:18909:24377_1:N:0:CAGATC NW_022994940.1 2 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1537:8332:6558_1:N:0:CAGATC NW_022994968.1 91857 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1627:20066:30044_1:N:0:CAGATC NW_022994814.1 2 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:1663:30083:18114_1:N:0:CAGATC NC_001276.1 18095 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2157:26413:34648_1:N:0:CAGATC NW_022994970.1 1 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2331:18304:31939_1:N:0:CAGATC NW_022994893.1 1 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2412:21558:8015_1:N:0:CAGATC NW_022994940.1 2 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2430:6451:17801_1:N:0:CAGATC NW_022994911.1 90087 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2443:12997:7842_1:N:0:CAGATC NW_022994928.1 69286 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2547:28429:14779_1:N:0:CAGATC NW_022994994.1 1 Chromosomal sequence could not be extracted for A00387:99:GW190426169th_novaxp:4:2578:23475:12555_1:N:0:CAGATC NW_022994924.1 1 Processed 58000000 sequence pairs so far 58618241 reads; of these: 58618241 (100.00%) were paired; of these: 58442519 (99.70%) aligned concordantly 0 times 113644 (0.19%) aligned concordantly exactly 1 time 62078 (0.11%) aligned concordantly >1 times 0.30% overall alignment rate 58618241 reads; of these: 58618241 (100.00%) were paired; of these: 58444737 (99.70%) aligned concordantly 0 times 109935 (0.19%) aligned concordantly exactly 1 time 63569 (0.11%) aligned concordantly >1 times 0.30% overall alignment rate 58618241 reads; of these: 58618241 (100.00%) were paired; of these: 31629127 (53.96%) aligned concordantly 0 times 12969973 (22.13%) aligned concordantly exactly 1 time 14019141 (23.92%) aligned concordantly >1 times 46.04% overall alignment rate 58618241 reads; of these: 58618241 (100.00%) were paired; of these: 31630548 (53.96%) aligned concordantly 0 times 12972417 (22.13%) aligned concordantly exactly 1 time 14015276 (23.91%) aligned concordantly >1 times 46.04% overall alignment rate Processed 58618241 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: 58618241 Number of paired-end alignments with a unique best hit: 34683710 Mapping efficiency: 59.2% Sequence pairs with no alignments under any condition: 18011074 Sequence pairs did not map uniquely: 5923457 Sequence pairs which were discarded because genomic sequence could not be extracted: 122 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 17340208 ((converted) top strand) GA/CT/CT: 3654 (complementary to (converted) top strand) GA/CT/GA: 4778 (complementary to (converted) bottom strand) CT/GA/GA: 17334948 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1484454964 Total methylated C's in CpG context: 22326558 Total methylated C's in CHG context: 2339845 Total methylated C's in CHH context: 10359171 Total methylated C's in Unknown context: 188436 Total unmethylated C's in CpG context: 154228298 Total unmethylated C's in CHG context: 241093267 Total unmethylated C's in CHH context: 1054107825 Total unmethylated C's in Unknown context: 4382777 C methylated in CpG context: 12.6% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 4.1% Bismark completed in 0d 6h 19m 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) 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-big'): /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-big 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 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 (56420801 sequences in total) 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 (56420801 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 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1103:8836:30158_1:N:0:ATGTCA NW_022994819.1 1 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1105:13798:23987_1:N:0:ATGTCA NW_022994947.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1106:10480:64720_1:N:0:ATGTCA NW_022994921.1 323372 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1112:11891:7110_1:N:0:ATGTCA NW_022994970.1 1 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1118:26808:21174_1:N:0:ATGTCA NW_022994935.1 43660 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1119:29356:45488_1:N:0:ATGTCA NW_022994994.1 3 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1201:21816:37172_1:N:0:ATGTCA NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1202:10927:16621_1:N:0:ATGTCA NW_022994946.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1203:7182:21948_1:N:0:ATGTCA NW_022994968.1 91854 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1205:25438:55508_1:N:0:ATGTCA NW_022994964.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1206:12347:26818_1:N:0:ATGTCA NW_022994908.1 34584 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1217:6766:21333_1:N:0:ATGTCA NW_022994940.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1219:10186:53240_1:N:0:ATGTCA NC_001276.1 18095 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1219:4340:56721_1:N:0:ATGTCA NC_001276.1 1 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1220:24992:58040_1:N:0:ATGTCA NW_022994933.1 29877 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1221:13281:16023_1:N:0:ATGTCA NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1222:8978:2979_1:N:0:ATGTCA NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1222:18122:4016_1:N:0:ATGTCA NW_022994972.1 189608 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1222:24860:14635_1:N:0:ATGTCA NW_022994968.1 91857 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1224:6441:45066_1:N:0:ATGTCA NW_022994921.1 323386 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2103:4391:13949_1:N:0:ATGTCA NW_022994921.1 323385 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2103:27225:29349_1:N:0:ATGTCA NW_022994904.1 192164 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2105:21278:52414_1:N:0:ATGTCA NW_022994931.1 118190 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2107:12702:27574_1:N:0:ATGTCA NW_022994968.1 91859 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2108:23216:13931_1:N:0:ATGTCA NW_022994980.1 2 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2109:28006:44978_1:N:0:ATGTCA NW_022994902.1 1 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2115:22871:17447_1:N:0:ATGTCA NW_022994997.1 297082 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2119:23206:41831_1:N:0:ATGTCA NW_022994966.1 514616 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2123:18700:31986_1:N:0:ATGTCA NW_022994804.1 1 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2124:26839:46894_1:N:0:ATGTCA NC_001276.1 1 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2202:10612:6548_1:N:0:ATGTCA NW_022994915.1 76356 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2202:4036:8587_1:N:0:ATGTCA NC_001276.1 2 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2209:1915:51289_1:N:0:ATGTCA NW_022994886.1 3 Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:2210:2930:24638_1:N:0:ATGTCA NW_022994814.1 1 Processed 21000000 sequence pairs so far slurmstepd: error: *** JOB 1966853 ON n2334 CANCELLED AT 2021-06-09T12:45:32 ***