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-chilean-mussel/data/Mchi/ (absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/project-chilean-mussel/data/Mchi/)' 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-chilean-mussel/output/07-bismark'): /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LYa_BSr3_R1.fastq.gz /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LYa_BSr3_R2.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-chilean-mussel/output/07-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-chilean-mussel/output/07-bismark Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/project-chilean-mussel/data/Mchi/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LYa_BSr3_R1.fastq.gz and /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LYa_BSr3_R2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file LYa_BSr3_R1.fastq.gz to LYa_BSr3_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file LYa_BSr3_R1.fastq.gz (100000000 sequences in total) Writing a G -> A converted version of the input file LYa_BSr3_R2.fastq.gz to LYa_BSr3_R2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file LYa_BSr3_R2.fastq.gz (100000000 sequences in total) Input files are LYa_BSr3_R1.fastq.gz_C_to_T.fastq and LYa_BSr3_R2.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-chilean-mussel/data/Mchi/ 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 LYa_BSr3_R1.fastq.gz_C_to_T.fastq and LYa_BSr3_R2.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: A01057:543:H2JCGDSXF:1:1101:1633:1000_1:N:0:NACGGCAT+TCACCAAT/1 77 * 0 0 * * 0 0 NATTAAATTGATTGAAAGATTATGTTTTTATTATATGAATATTAGGTATAATTTTTTATTTGAAGTGGTGGTTGTATGGTAGGATATTATAGGGAATATATGTATTAAGTTTTAAGTTGATTGGATTTTAATTTTATTAAAAATTATTTTG #FFFFFFFF:F,FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF,FF: YT:Z:UP A01057:543:H2JCGDSXF:1:1101:1633:1000_2:N:0:NACGGCAT+TCACCAAT/2 141 * 0 0 * * 0 0 NAAAAAAAAAAAAAAACACTCAAAATTAAACTTTTTAATCAAAATAATTTTTAATAAAATTAAAATCCANTCAACTTAAAACTTAATACATATATTACCTATAATATCCTACCATACAACCACCACTTCAAATAAAAAATTATACCTAATA #FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF#FFFFF:FFFFFF:FFF:FFF:FFFFF,FFFFFFFFF,,FFFF:FFFFFFFFF:FFFFFFFF:F:FF:FFFF,FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from LYa_BSr3_R1.fastq.gz_C_to_T.fastq and LYa_BSr3_R2.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: A01057:543:H2JCGDSXF:1:1101:1633:1000_1:N:0:NACGGCAT+TCACCAAT/1 83 Chromosome_2_GA_converted 11517835 0 119M10I22M = 11517806 -170 CAAAATAATTTTTAATAAAATTAAAATCCAATCAACTTAAAACTTAATACATATATTCCCTATAATATCCTACCATACAACCACCACTTCAAATAAAAAATTATACCTAATATTCATATAATAAAAACATAATCTTTCAATCAATTTAATN :FF,FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF,F:FFFFFFFF# AS:i:-66 XS:i:-66 XN:i:0 XM:i:6 XO:i:1 XG:i:10 NM:i:16 MD:Z:27T30T8C12T39C19T0 YS:i:-91 YT:Z:CP A01057:543:H2JCGDSXF:1:1101:1633:1000_2:N:0:NACGGCAT+TCACCAAT/2 163 Chromosome_2_GA_converted 11517806 0 4M10I137M = 11517835 170 NAAAAAAAAAAAAAAACACTCAAAATTAAACTTTTTAATCAAAATAATTTTTAATAAAATTAAAATCCANTCAACTTAAAACTTAATACATATATTACCTATAATATCCTACCATACAACCACCACTTCAAATAAAAAATTATACCTAATA #FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF#FFFFF:FFFFFF:FFF:FFF:FFFFF,FFFFFFFFF,,FFFF:FFFFFFFFF:FFFFFFFF:F:FF:FFFF,FFFFFFFFF AS:i:-91 XS:i:-91 XN:i:0 XM:i:11 XO:i:1 XG:i:10 NM:i:21 MD:Z:0T2T0T0C5C44T2A26C0T8C12T31 YS:i:-66 YT:Z:CP >>> Writing bisulfite mapping results to LYa_BSr3_pe.bam <<< Reading in the sequence files /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LYa_BSr3_R1.fastq.gz and /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LYa_BSr3_R2.fastq.gz Chromosomal sequence could not be extracted for A01057:543:H2JCGDSXF:1:1102:9046:24956_1:N:0:CACGGCAT+TCACCAAT Chromosome_1 1 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 A01057:543:H2JCGDSXF:1:1134:21585:18427_1:N:0:CACGGCAT+TCACCAAT Chromosome_1 1 Processed 5000000 sequence pairs so far 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 A01057:543:H2JCGDSXF:1:1172:10357:15953_1:N:0:CACGGCAT+TCACCAAT Chromosome_3 154668910 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far 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 A01057:543:H2JCGDSXF:1:1409:12744:10598_1:N:0:CACGGCAT+TCACCAAT Chromosome_9 133209673 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far 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 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 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A01057:543:H2JCGDSXF:1:1578:3323:1861_1:N:0:CACGGCAT+TCACCAAT Chromosome_1 1 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far