Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/srlab/programs/samtools-1.20/samtools' Reference genome folder provided is /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/data/genome/ (absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/data/genome/)' FastQ format assumed (by default) Attention: early reports suggested that high values of -p to have diminishing returns. Please test different values using a small subset of data for your hardware setting. Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/output/16-bismark'): /mmfs1/gscratch/coenv/sr320/cod-bs/51B_1.fastq.gz /mmfs1/gscratch/coenv/sr320/cod-bs/51B_2.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/output/16-bismark/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/output/16-bismark Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/data/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /mmfs1/gscratch/coenv/sr320/cod-bs/51B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/51B_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 51B_1.fastq.gz to 51B_1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 51B_1.fastq.gz (71804292 sequences in total) Writing a G -> A converted version of the input file 51B_2.fastq.gz to 51B_2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 51B_2.fastq.gz (71804292 sequences in total) Input files are 51B_1.fastq.gz_C_to_T.fastq and 51B_2.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/data/genome/ with the specified options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 51B_1.fastq.gz_C_to_T.fastq and 51B_2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00160:538:22WG5VLT4:6:1101:22679:1042_1:N:0:GAATCCGA+AGNTAGTG/1 99 NC_082393.1_CT_converted 13279022 25 151M = 13279085 214 GNAGTTTATAGTGTATTGTATTAATAAGTTTATATTTATTAATGTGAATTTTGGGTTTGTATATTTATAGTTAGGGTTTGAATGTTAGGTGTAATATGAATGATAGTTAGTTTAAGTGGTTGTTTATTTTTAGTTTGTTGTGTGTTTTTGT I#IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-1 XS:i:-69 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:1T149 YS:i:-18 YT:Z:CP LH00160:538:22WG5VLT4:6:1101:22679:1042_2:N:0:GAATCCGA+AGNTAGTG/2 147 NC_082393.1_CT_converted 13279085 25 151M = 13279022 -214 TTTATAGTTAGGGTTTGAATGTTAGGTGTAATATGAATGATAGTTAGTTTAAGTGGTTGTTTATTTTTAGTTTGTTGTGTGTTTTTGTTTTGATGGTGATAGGTGTGTTGAATGGTAGTAATGTATTTGTGAATTGATGTGATTTTTTTTT IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I-III9I AS:i:-18 XS:i:-80 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:144G0A3G1 YS:i:-1 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 51B_1.fastq.gz_C_to_T.fastq and 51B_2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00160:538:22WG5VLT4:6:1101:22679:1042_1:N:0:GAATCCGA+AGNTAGTG/1 83 NC_082396.1_GA_converted 19142547 0 6M2I28M1D115M = 19142484 -213 ACAAAAACACACAACAAACTAAAAATAAACAACCACTTAAACTAACTATCATTCATATTACACCTAACATTCAAACCCTAACTATAAATATACAAACCCAAAATTCACATTAATAAATATAAACTTATTAATACAATACACTATAAACTNC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII#I AS:i:-62 XS:i:-82 XN:i:0 XM:i:8 XO:i:2 XG:i:3 NM:i:11 MD:Z:25C5A2^T36C51C9C5A5T2A1 YS:i:-79 YT:Z:CP LH00160:538:22WG5VLT4:6:1101:22679:1042_2:N:0:GAATCCGA+AGNTAGTG/2 163 NC_082396.1_GA_converted 19142484 0 69M2I28M1D52M = 19142547 213 AAAAAAAAATCACATCAATTCACAAATACATTACTACCATTCAACACACCTATCACCATCAAAACAAAAACACACAACAAACTAAAAATAAACAACCACTTAAACTAACTATCATTCATATTACACCTAACATTCAAACCCTAACTATAAA I9III-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII AS:i:-79 XS:i:-111 XN:i:0 XM:i:10 XO:i:2 XG:i:3 NM:i:13 MD:Z:1C3T0C4C15C5T15T38C5A2^T36C15 YS:i:-62 YT:Z:CP >>> Writing bisulfite mapping results to 51B_pe.bam <<< Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/51B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/51B_2.fastq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1124:26709:6029_1:N:0:GAATCCGA+AGCTAGTG NC_036931.1 16417 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1148:13446:26914_1:N:0:GAATCCGA+AGCTAGTG NC_082394.1 22312304 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1158:7369:27321_1:N:0:GAATCCGA+AGCTAGTG NC_082400.1 17993487 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1158:7360:27335_1:N:0:GAATCCGA+AGCTAGTG NC_082400.1 17993487 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1176:8793:1434_1:N:0:GAATCCGA+AGCTAGTG NC_082387.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1176:8809:1434_1:N:0:GAATCCGA+AGCTAGTG NC_082387.1 2 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1192:45920:11744_1:N:0:GAATCCGA+AGCTAGTG NC_082390.1 23393725 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1204:30642:20765_1:N:0:GAATCCGA+AACTAGTG NC_082394.1 22312317 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1205:39025:29114_1:N:0:GAATCCGA+AGCTAGTG NC_082399.1 21077819 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1234:47215:29562_1:N:0:GAATCCGA+AGCTAGTG NC_082398.1 16295396 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1242:23432:16353_1:N:0:GAATCCGA+AGCTAGTG NC_082394.1 22312303 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1249:48946:23230_1:N:0:GAATCCGA+AGCTAGTG NC_082399.1 21077815 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1253:3104:15064_1:N:0:TAATCCGA+AGCTAGTG NC_082399.1 21077819 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1261:41291:9082_1:N:0:GAATCCGA+AGCTAGTG NC_082399.1 21077814 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1271:22566:17655_1:N:0:GAATCCGA+AGCTAGTG NC_082396.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1277:44350:3788_1:N:0:GAATCCGA+AGCTAGTG NC_082400.1 17993471 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1283:38475:28273_1:N:0:GAATCCGA+AGCTAGTG NC_082392.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1283:38483:28287_1:N:0:GAATCCGA+AGCTAGTG NC_082392.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1288:26798:13159_1:N:0:GAATCCGA+AGCTAGTG NC_082400.1 17993471 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1289:1510:28273_1:N:0:GAATCCGA+AGCTAGTG NC_082402.1 1 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1297:20365:26452_1:N:0:GAATCCGA+AGCTAGTG NC_082383.1 23805011 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1305:8995:23020_1:N:0:GAATCCGA+AGCTAGTG NC_082396.1 24646066 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1307:20753:3003_1:N:0:GAATCCGA+AGCTAGTG NC_082399.1 21077817 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1311:50889:27181_1:N:0:GAATCCGA+AGCTAGTG NC_082395.1 26048656 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1315:9756:5959_1:N:0:GAATCCGA+AGCTAGTG NC_082399.1 21077815 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1337:41008:3886_1:N:0:GAATCCGA+AGCTAGTG NC_082399.1 21077809 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1340:16642:26172_1:N:0:GAATCCGA+AGCTAGTG NC_082399.1 21077812 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1354:42910:28049_1:N:0:GAATCCGA+AGCTAGTG NC_082390.1 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1360:38920:21087_1:N:0:GAATCCGA+AGCTAGTG NC_082390.1 23393720 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1360:38936:21087_1:N:0:GAATCCGA+AGCTAGTG NC_082390.1 23393720 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1362:29493:10427_1:N:0:GAATCCGA+AGCTAGTG NC_082399.1 21077815 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1384:39916:21577_1:N:0:GAATCCGA+AGCTAGTG NC_082387.1 1 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1397:44310:21844_1:N:0:GAATCCGA+AGCTAGTG NC_082399.1 21077815 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1402:12216:28932_1:N:0:GAATCCGA+AGCTAGTG NC_082383.1 23805026 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1408:14846:3535_1:N:0:GAATCCGA+AGCTAGTG NC_082398.1 16295404 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1417:27583:10735_1:N:0:GAATCCGA+AGCTAGTG NC_082396.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1418:2173:14097_1:N:0:GAATCCGA+AGCTAGTG NC_036931.1 16431 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1422:37714:7233_1:N:0:GAATCCGA+AGCTAGTG NC_082400.1 17993481 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1424:33587:13453_1:N:0:GAATCCGA+AGCTAGTG NC_082396.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1424:33604:13453_1:N:0:GAATCCGA+AGCTAGTG NC_082396.1 2 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1445:24200:18636_1:N:0:GAATCCGA+AGCTAGTG NC_082401.1 1 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1452:33094:16689_1:N:0:GAATCCGA+AGCTAGTG NC_082399.1 21077815 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1458:4285:29492_1:N:0:GAATCCGA+AGCTAGTG NC_082395.1 26048639 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1461:20438:15904_1:N:0:GAATCCGA+AGCTAGTG NC_036931.1 16430 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1481:39616:5006_1:N:0:GAATCCGA+AGCTAGTG NC_082387.1 2 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1489:22517:19588_1:N:0:GAATCCGA+AGCTAGTG NC_082382.1 26289593 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2124:17371:23118_1:N:0:GAATCCGA+AGCTAGTG NC_082400.1 17993494 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2136:37536:9363_1:N:0:GAATCCGA+AGCTAGTG NC_082382.1 26289593 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2152:15679:17361_1:N:0:GAATCCGA+AGCTAGTG NC_082393.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2160:33701:28581_1:N:0:GAATCCGA+AGCTAGTG NC_082393.1 1 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2171:12807:27937_1:N:0:GAATCCGA+AGCTAGTG NC_082394.1 22312303 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2196:3751:20079_1:N:0:GAATCCGA+AGCTAGTG NC_082387.1 1 Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2236:45370:6617_1:N:0:GAATCCGA+AGCTAGTG NC_082394.1 22312307 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2245:40369:1238_1:N:0:GAATCCGA+AGCTAGTG NC_082398.1 16295397 Processed 50000000 sequence pairs so far