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/36B_1.fastq.gz /mmfs1/gscratch/coenv/sr320/cod-bs/36B_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/36B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/36B_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 36B_1.fastq.gz to 36B_1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 36B_1.fastq.gz (67535875 sequences in total) Writing a G -> A converted version of the input file 36B_2.fastq.gz to 36B_2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 36B_2.fastq.gz (67535875 sequences in total) Input files are 36B_1.fastq.gz_C_to_T.fastq and 36B_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 36B_1.fastq.gz_C_to_T.fastq and 36B_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: LH00160:538:22WG5VLT4:6:1101:24459:1042_1:N:0:ATCCAGAG+TANCGTCG/1 77 * 0 0 * * 0 0 ANATATATGGATGTATATGGGGTTTGTGATAAGGGGTGTGTGTGTGTGTGTGTGGGGGGGGGGGGGGTTTTGTTTGTGTGTGTGTGTTTTTGTGTGTTTTTTTTTGTTTGTTTTTTTTTGTTTGTGTTTTTGTGTGTTTTTTTTTTATTAG I#9IIIII9II9I99IIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIIIIIII9-I9III9I-I---99--9---9---9---9-9--99--99-9---9-I------9----9-99I99-9---9--9--9------9- YT:Z:UP LH00160:538:22WG5VLT4:6:1101:24459:1042_2:N:0:ATCCAGAG+TANCGTCG/2 141 * 0 0 * * 0 0 AAAAAAATTTTAAATCTTTAAACAATAAATATAAAAACTACTATATATATATATATTTTTTTTTTATAAATTTCACACTTAATAACATATTAATATACCATAAAATTTTTTCCTTATCTAAAATATACCATAACACAAAAAAAATCAAAAA IIIIIIIIIIIIIIIIIIIIIIIII-I-IIIIIIIII9II-IIIIIIIIIIII9IIIII99IIIIIIII-IIIIIIIIIIIIIII-II9III9IIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIII9IIII-9I-II9I9IIIII9I9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 36B_1.fastq.gz_C_to_T.fastq and 36B_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: LH00160:538:22WG5VLT4:6:1101:24459:1042_1:N:0:ATCCAGAG+TANCGTCG/1 83 NC_082399.1_GA_converted 3555689 8 49M1D1M1D101M = 3555535 -307 CTAATAAAAAAAAAACACACAAAAACACAAACAAAAAAAAACAAACAAAAAAAAACACACAAAAACACACACACACAAACAAAACCCCCCCCCCCCCCACACACACACACACACACCCCTTATCACAAACCCCATATACATCCATATATNT -9------9--9--9---9-99I99-9----9------I-9---9-99--99--9-9---9---9---9--99---I-I9III9I-9IIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIII99I9II9IIIII9#I AS:i:-119 XN:i:0 XM:i:18 XO:i:2 XG:i:2 NM:i:20 MD:Z:6T4C1C7C7C3C1C1C1C3C5^C1^C1C1C7C1C13C5C14C50A1 YS:i:-6 YT:Z:CP LH00160:538:22WG5VLT4:6:1101:24459:1042_2:N:0:ATCCAGAG+TANCGTCG/2 163 NC_082399.1_GA_converted 3555535 8 151M = 3555689 307 AAAAAAATTTTAAATCTTTAAACAATAAATATAAAAACTACTATATATATATATATTTTTTTTTTATAAATTTCACACTTAATAACATATTAATATACCATAAAATTTTTTCCTTATCTAAAATATACCATAACACAAAAAAAATCAAAAA IIIIIIIIIIIIIIIIIIIIIIIII-I-IIIIIIIII9II-IIIIIIIIIIII9IIIII99IIIIIIII-IIIIIIIIIIIIIII-II9III9IIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIII9IIII-9I-II9I9IIIII9I9I AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:3T147 YS:i:-119 YT:Z:CP >>> Writing bisulfite mapping results to 36B_pe.bam <<< Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/36B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/36B_2.fastq.gz Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1111:12361:16941_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1112:28449:1112_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 3 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1114:15971:9489_1:N:0:ATCCGGAG+TAACGTCG NC_082394.1 22312320 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1123:31726:24911_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16451 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1160:15574:8970_1:N:0:ATCCAGAG+TAACGTCG NC_082383.1 23804995 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1181:29897:28581_1:N:0:ATCCAGAG+TAACGTCG NC_082387.1 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1192:20648:1784_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16435 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1193:14101:7878_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16422 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1193:14943:13005_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16427 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1196:38038:4320_1:N:0:ATCCAGAG+TAACGTCG NC_082388.1 28186518 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1205:13057:23356_1:N:0:ATCCAGAG+TAACGTCG NC_082392.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1212:37698:4068_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 1 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1226:31071:21451_1:N:0:ATCCAGAG+TAACGTCG NC_082390.1 23393739 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1234:21295:1308_1:N:0:ATCCAGAG+TAACGTCG NC_082400.1 17993479 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1250:37755:27867_1:N:0:ATCCAGAG+TAACGTCG NC_082382.1 26289599 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1253:48372:19518_1:N:0:ATCCAGAG+TAACGTCG NC_082388.1 28186540 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1253:13163:25191_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16434 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1259:33110:16605_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16422 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1268:45240:11212_1:N:0:ATCCAGAG+TAACATCG NC_082396.1 2 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1276:26968:24687_1:N:0:ATCCAGAG+TAACGTCG NC_082398.1 16295385 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1284:21765:8704_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 1 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1294:13648:13369_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 1 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1333:31330:17921_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16423 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1338:35934:24295_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16423 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1342:14150:19196_1:N:0:ATCCAGAG+TAACGTCG NC_082387.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1343:48922:11450_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16439 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1345:14506:7878_1:N:0:ATCCAGAG+TAACGTCG NC_082385.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1346:43007:9867_1:N:0:ATCCAGAG+TAACGTCG NC_082390.1 23393716 Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1362:14441:17347_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 1 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1398:3314:13943_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16451 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1414:25997:6281_1:N:0:ATCCAGAG+TAACGTCG NC_082399.1 21077817 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1423:42214:16535_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16446 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1426:7255:9139_1:N:0:ATCCAGAG+TAACGTCG NC_082402.1 19478585 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1426:7247:9153_1:N:0:ATCCGGAG+TAACGTCG NC_082402.1 19478585 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1446:14085:6393_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16419 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1456:51002:23426_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16431 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1464:44115:11730_1:N:0:ATCCAGAG+TAACGTCG NC_082382.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1468:4973:26424_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1468:4981:26438_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1472:26070:7444_1:N:0:ATCCAGAG+TAACGTCG NC_082400.1 17993475 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1484:32098:20205_1:N:0:ATCCAGAG+TAACGTCG NC_082383.1 1 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1494:6147:29380_1:N:0:GTCCAGAG+TAACGTCG NC_082385.1 3 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2105:7619:4082_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16438 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2121:36404:3423_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16423 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2122:15509:6001_1:N:0:ATCCAGAG+TAACGTCG NC_082387.1 2 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2124:29630:15904_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16426 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2129:40765:22516_1:N:0:ATCCAGAG+TAACGTCG NC_082399.1 21077814 Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2183:39988:3830_1:N:0:ATCCAGAG+TAACGTCG NC_036931.1 16451 Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2210:10476:3507_1:N:0:ATCCAGAG+TAACGTCG NC_082402.1 19478582 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2210:44779:20919_1:N:0:ATCCAGAG+TAACGTCG NC_082399.1 21077820 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2220:1308:23525_1:N:0:ATCAAGAG+TAACGTCG NC_082393.1 3 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2224:16764:3605_1:N:0:ATCCAGAG+TAACGTCG NC_082389.1 23759922 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2225:9351:1756_1:N:0:ATCCAGAG+TAACGTNG NC_082387.1 1 Processed 46000000 sequence pairs so far