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 ../../data/genome/ (absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/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/ceasmallr/output/05-bismark-align-full'): ../../data/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz ../../data/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.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 Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/output/05-bismark-align-full/ 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/ceasmallr/output/05-bismark-align-full Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/data/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../../data/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz to CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz to CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz (134159156 sequences in total) Writing a C -> T converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz to CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz to CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz (134159156 sequences in total) Input files are CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/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 CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.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: GWNJ-1012:512:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ANATTAATTTTTATAATTAATAAATTTTTTTATTATAAAAATATTATTTTTAATAAATAATTTAAAATAATTTATTAAAATATAATAATTTTTATTATAAAAAAAATTATATTTTTAATAATTTAAAATTTATTAATATAATATTATAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTTTTAATAATATTTATTATTAAATTATTTTATTTTATAATTTATAATATTATATTAATAAATTTTAAATTATTAAAAATATAATTTTTTTTATAATAAAAATTATTATATTTTAATAAATTATTTTAAAATATTTATTAAAAATAATAT :F:FFF:FFFFF:FFFFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.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: GWNJ-1012:512:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ANATTAATTTTTATAATTAATAAATTTCCTCACTATAAAAATACTATCTCCAACAAACAATCCAAAACAATTTACCAAAATACAATAATTCCTATTATAAAAAAAATTATACTCTCAATAATCCAAAATTTATCAACATAACACCACAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTTTTGGTGATATTTATTGTTGAATTGTTTTGTTTTATAGTTTGTGGTGTTATGTTGATAAATTTTGGATTATTGAGAGTATAATTTTTTTTATAATAGGAATTATTGTATTTTGGTAAATTGTTTTGGAGTGTTTGTTGGAGATAGTAT :F:FFF:FFFFF:FFFFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.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: GWNJ-1012:512:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ANATTAATTTTTATAATTAATAAATTTCCTCACTATAAAAATACTATCTCCAACAAACAATCCAAAACAATTTACCAAAATACAATAATTCCTATTATAAAAAAAATTATACTCTCAATAATCCAAAATTTATCAACATAACACCACAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTTTTGGTGATATTTATTGTTGAATTGTTTTGTTTTATAGTTTGTGGTGTTATGTTGATAAATTTTGGATTATTGAGAGTATAATTTTTTTTATAATAGGAATTATTGTATTTTGGTAAATTGTTTTGGAGTGTTTGTTGGAGATAGTAT :F:FFF:FFFFF:FFFFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.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: GWNJ-1012:512:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ANATTAATTTTTATAATTAATAAATTTTTTTATTATAAAAATATTATTTTTAATAAATAATTTAAAATAATTTATTAAAATATAATAATTTTTATTATAAAAAAAATTATATTTTTAATAATTTAAAATTTATTAATATAATATTATAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTTTTAATAATATTTATTATTAAATTATTTTATTTTATAATTTATAATATTATATTAATAAATTTTAAATTATTAAAAATATAATTTTTTTTATAATAAAAATTATTATATTTTAATAAATTATTTTAAAATATTTATTAAAAATAATAT :F:FFF:FFFFF:FFFFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP >>> Writing bisulfite mapping results to CF01-CM02-Larvae_pe.bam <<< Reading in the sequence files ../../data/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1116:7292:4977_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1116:7274:6198_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1129:11107:29371_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1129:10809:29700_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1129:11225:30138_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1137:29396:17989_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1151:28076:7216_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1163:11921:2566_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1175:18032:33004_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1228:12671:16611_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 3 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1260:1868:24048_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1263:25852:3427_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1263:14145:32816_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1321:3558:21402_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1321:3676:21856_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1326:17589:19805_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1341:14109:27336_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1344:28772:19946_1:N:0:ACACGGAC+TGCGAGAC NC_035780.1 2 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1355:21197:17503_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 3 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1420:3685:25911_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1420:4282:26694_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1432:9001:34554_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1461:11577:15217_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1476:16767:13213_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1543:16016:18114_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1560:21414:24017_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1560:23222:24236_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 3 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:9227:11083_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:8070:12524_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1610:9634:21120_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1610:9986:27336_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1669:18548:7780_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2158:31277:36558_1:N:0:GCACGGAC+TGCGAGAC NC_035781.1 3 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2213:20844:17707_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2213:20980:17754_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2272:29975:21465_1:N:0:GCACAGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2305:17002:1063_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2307:23330:19006_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2307:23393:21684_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 48000000 sequence pairs so far