Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/bin/samtools' Reference genome folder provided is ../../data/Haws-10/ (absolute path is '/home/shared/16TB_HDD_01/sr320/github/project-oyster-oa/data/Haws-10/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 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 '/home/shared/16TB_HDD_01/sr320/github/project-oyster-oa/code/Haws'): ../../data/Haws-10/zr3644_9_R1_val_1_val_1_val_1.fq.gz ../../data/Haws-10/zr3644_9_R2_val_2_val_2_val_2.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: /home/shared/16TB_HDD_01/sr320/github/project-oyster-oa/analyses/Haws-10/ 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: /home/shared/16TB_HDD_01/sr320/github/project-oyster-oa/code/Haws Now reading in and storing sequence information of the genome specified in: /home/shared/16TB_HDD_01/sr320/github/project-oyster-oa/data/Haws-10/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../../data/Haws-10/zr3644_9_R1_val_1_val_1_val_1.fq.gz and ../../data/Haws-10/zr3644_9_R2_val_2_val_2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3644_9_R1_val_1_val_1_val_1.fq.gz to zr3644_9_R1_val_1_val_1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_9_R1_val_1_val_1_val_1.fq.gz to zr3644_9_R1_val_1_val_1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_9_R1_val_1_val_1_val_1.fq.gz (47573665 sequences in total) Writing a C -> T converted version of the input file zr3644_9_R2_val_2_val_2_val_2.fq.gz to zr3644_9_R2_val_2_val_2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_9_R2_val_2_val_2_val_2.fq.gz to zr3644_9_R2_val_2_val_2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_9_R2_val_2_val_2_val_2.fq.gz (47573665 sequences in total) Input files are zr3644_9_R1_val_1_val_1_val_1.fq.gz_C_to_T.fastq and zr3644_9_R1_val_1_val_1_val_1.fq.gz_G_to_A.fastq and zr3644_9_R2_val_2_val_2_val_2.fq.gz_C_to_T.fastq and zr3644_9_R2_val_2_val_2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/16TB_HDD_01/sr320/github/project-oyster-oa/data/Haws-10/ 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 zr3644_9_R1_val_1_val_1_val_1.fq.gz_C_to_T.fastq and zr3644_9_R2_val_2_val_2_val_2.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: A00742:173:HMGVGDSXY:2:1101:6008:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 77 * 0 0 * * 0 0 ATTTTTATATTTTATATATTTATAAATTTAAATTAATTTTTTTTTAATTTTATATAATAAATAATTATAATTTTTATAATTTAAATAATAAAAAATATAAAATTAATTAATTAT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:6008:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 141 * 0 0 * * 0 0 TTTTTATAAATAAAAATATATTTTTTTTAATATATAATATAAATATTTTTAAAATAAATTTAAAAAATTTATAATTAATTAATTTTATATTTTTTATTATTTAAATTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_9_R1_val_1_val_1_val_1.fq.gz_G_to_A.fastq and zr3644_9_R2_val_2_val_2_val_2.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: A00742:173:HMGVGDSXY:2:1101:6008:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 77 * 0 0 * * 0 0 ATTTTTATATTCCACATACTTACAAATCTAAATCAACTCTTTTTTAATTTTACACAATAAATAACTATAATCTTTATAACTTAAATAATAAAAAACATAAAATTAATTAACCAC FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:6008:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 141 * 0 0 * * 0 0 TTTTTGTGAATAGAGATATGTTTTTTTTGATGTATGATGTAAATATTTTTGAAATGAATTTGAAAAGTTTGTGGTTAATTAATTTTATGTTTTTTATTATTTAAGTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_9_R1_val_1_val_1_val_1.fq.gz_G_to_A.fastq and zr3644_9_R2_val_2_val_2_val_2.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: A00742:173:HMGVGDSXY:2:1101:6008:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 77 * 0 0 * * 0 0 ATTTTTATATTCCACATACTTACAAATCTAAATCAACTCTTTTTTAATTTTACACAATAAATAACTATAATCTTTATAACTTAAATAATAAAAAACATAAAATTAATTAACCAC FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:6008:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 141 * 0 0 * * 0 0 TTTTTGTGAATAGAGATATGTTTTTTTTGATGTATGATGTAAATATTTTTGAAATGAATTTGAAAAGTTTGTGGTTAATTAATTTTATGTTTTTTATTATTTAAGTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_9_R1_val_1_val_1_val_1.fq.gz_C_to_T.fastq and zr3644_9_R2_val_2_val_2_val_2.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: A00742:173:HMGVGDSXY:2:1101:6008:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 77 * 0 0 * * 0 0 ATTTTTATATTTTATATATTTATAAATTTAAATTAATTTTTTTTTAATTTTATATAATAAATAATTATAATTTTTATAATTTAAATAATAAAAAATATAAAATTAATTAATTAT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:6008:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 141 * 0 0 * * 0 0 TTTTTATAAATAAAAATATATTTTTTTTAATATATAATATAAATATTTTTAAAATAAATTTAAAAAATTTATAATTAATTAATTTTATATTTTTTATTATTTAAATTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_9_pe.bam <<< Reading in the sequence files ../../data/Haws-10/zr3644_9_R1_val_1_val_1_val_1.fq.gz and ../../data/Haws-10/zr3644_9_R2_val_2_val_2_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1123:4426:34491_1:N:0:TGTCGCTG+AGTCAGAC NW_027062570.1 3947 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1363:19651:25692_1:N:0:TGTCGCTG+AGTCAGAC NW_027062580.1 24116 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 Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1532:9136:27211_1:N:0:TGTCGCTG+AGTCAGAC NW_027062570.1 3942 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 A00742:173:HMGVGDSXY:2:1610:29523:1736_1:N:0:TGTCGCTG+AGTCAGAC NW_027062578.1 34406 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 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:2249:2736:2221_1:N:0:TGTCGCTG+AGTCAGAC NW_027062570.1 3928 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:2357:3549:26866_1:N:0:TGTCGCTG+AGTCAGAC NW_027062568.1 15471 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 Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:2546:27778:20071_1:N:0:TGTCGCTG+AGTCAGAC NW_027062573.1 1893 Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:2547:12002:29230_1:N:0:TGTCGCTG+AGTCAGAC NW_027062578.1 34394 Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:2645:30816:35571_1:N:0:TGTCGCTG+AGTCAGAC NW_027062569.1 1 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far 47573665 reads; of these: 47573665 (100.00%) were paired; of these: 33797513 (71.04%) aligned concordantly 0 times 5795952 (12.18%) aligned concordantly exactly 1 time 7980200 (16.77%) aligned concordantly >1 times 28.96% overall alignment rate 47573665 reads; of these: 47573665 (100.00%) were paired; of these: 33699529 (70.84%) aligned concordantly 0 times 5829790 (12.25%) aligned concordantly exactly 1 time 8044346 (16.91%) aligned concordantly >1 times 29.16% overall alignment rate 47573665 reads; of these: 47573665 (100.00%) were paired; of these: 33772000 (70.99%) aligned concordantly 0 times 5792473 (12.18%) aligned concordantly exactly 1 time 8009192 (16.84%) aligned concordantly >1 times 29.01% overall alignment rate 47573665 reads; of these: 47573665 (100.00%) were paired; of these: 33674341 (70.78%) aligned concordantly 0 times 5828398 (12.25%) aligned concordantly exactly 1 time 8070926 (16.97%) aligned concordantly >1 times 29.22% overall alignment rate Processed 47573665 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 190294660. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 190294660. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 190294660. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 190294660. Successfully deleted the temporary files zr3644_9_R1_val_1_val_1_val_1.fq.gz_C_to_T.fastq, zr3644_9_R1_val_1_val_1_val_1.fq.gz_G_to_A.fastq, zr3644_9_R2_val_2_val_2_val_2.fq.gz_C_to_T.fastq and zr3644_9_R2_val_2_val_2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 47573665 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1035478149 Total methylated C's in CpG context: 14666819 Total methylated C's in CHG context: 885902 Total methylated C's in CHH context: 3967680 Total methylated C's in Unknown context: 66754 Total unmethylated C's in CpG context: 118267375 Total unmethylated C's in CHG context: 179896807 Total unmethylated C's in CHH context: 717793566 Total unmethylated C's in Unknown context: 3384797 C methylated in CpG context: 11.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.9% Bismark completed in 0d 4h 8m 13s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe