Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/caligus/genome/ (absolute path is '/gscratch/srlab/sr320/data/caligus/genome/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/0101b'): /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R1_001.fastq.gz /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R2_001.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!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/0101b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/caligus/genome/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Sealice_F1_S20_L001_R1_001.fastq.gz to Sealice_F1_S20_L001_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file Sealice_F1_S20_L001_R1_001.fastq.gz (113474961 sequences in total) Writing a G -> A converted version of the input file Sealice_F1_S20_L001_R2_001.fastq.gz to Sealice_F1_S20_L001_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file Sealice_F1_S20_L001_R2_001.fastq.gz (113474961 sequences in total) Input files are Sealice_F1_S20_L001_R1_001.fastq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/caligus/genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L001_R1_001.fastq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTTAGATTGGAAGAGTATATGTTTGAATTTTAGTTATGTGGTTATTTTGTAT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:FFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATAAAATCAAAAAAACATCATATAAAAAAAAAATATAAATCTCAATAATCAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L001_R1_001.fastq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1316:1016_1:N:0:NTGGCC/1 77 * 0 0 * * 0 0 TNTTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTTAGATTGGAAGAGTATATGTTTGAATTTTAGTTATGTGGTTATTTTGTAT F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:FFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1316:1016_2:N:0:NTGGCC/2 141 * 0 0 * * 0 0 AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATAAAATCAAAAAAACATCATATAAAAAAAAAATATAAATCTCAATAATCAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R2_001.fastq.gz Processed 1000000 sequence pairs so far 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 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 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 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 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Processed 108000000 sequence pairs so far Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Processed 111000000 sequence pairs so far Processed 112000000 sequence pairs so far Processed 113000000 sequence pairs so far 113474961 reads; of these: 113474961 (100.00%) were paired; of these: 101246787 (89.22%) aligned concordantly 0 times 3129530 (2.76%) aligned concordantly exactly 1 time 9098644 (8.02%) aligned concordantly >1 times 10.78% overall alignment rate 113474961 reads; of these: 113474961 (100.00%) were paired; of these: 101237532 (89.22%) aligned concordantly 0 times 3130887 (2.76%) aligned concordantly exactly 1 time 9106542 (8.03%) aligned concordantly >1 times 10.78% overall alignment rate Processed 113474961 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L001_R1_001.fastq.gz_C_to_T.fastq and Sealice_F1_S20_L001_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 113474961 Number of paired-end alignments with a unique best hit: 10187887 Mapping efficiency: 9.0% Sequence pairs with no alignments under any condition: 98364893 Sequence pairs did not map uniquely: 4922181 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5078535 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5109352 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 551028968 Total methylated C's in CpG context: 2494944 Total methylated C's in CHG context: 2053619 Total methylated C's in CHH context: 9741369 Total methylated C's in Unknown context: 1772643 Total unmethylated C's in CpG context: 81596268 Total unmethylated C's in CHG context: 85842553 Total unmethylated C's in CHH context: 369300215 Total unmethylated C's in Unknown context: 5582101 C methylated in CpG context: 3.0% C methylated in CHG context: 2.3% C methylated in CHH context: 2.6% C methylated in unknown context (CN or CHN): 24.1% Bismark completed in 0d 6h 38m 17s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/caligus/genome/ (absolute path is '/gscratch/srlab/sr320/data/caligus/genome/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/0101b'): /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R1_001.fastq.gz /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R2_001.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!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/0101b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/caligus/genome/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Sealice_F1_S20_L002_R1_001.fastq.gz to Sealice_F1_S20_L002_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file Sealice_F1_S20_L002_R1_001.fastq.gz (112706276 sequences in total) Writing a G -> A converted version of the input file Sealice_F1_S20_L002_R2_001.fastq.gz to Sealice_F1_S20_L002_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file Sealice_F1_S20_L002_R2_001.fastq.gz (112706276 sequences in total) Input files are Sealice_F1_S20_L002_R1_001.fastq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/caligus/genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_L002_R1_001.fastq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTATA F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_L002_R1_001.fastq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1081:1016_1:N:0:GTGGCC/1 77 * 0 0 * * 0 0 TNATTATTTTTTAATTTTTTTTAATTTATTTTTAAATTTTGTTTTTTTTAGGAAGTGTTAGGTATAATTTTGTTTGGTATAAAATAAATAAAGGATTAATTTTATTTTATAAGTTATTTATTTTATATTATTGAGTTTGAAGGTTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:F,FFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFF:F,FFFFFFFFF:FFF,FFFFF::F,FFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1081:1016_2:N:0:GTGGCC/2 141 * 0 0 * * 0 0 TCCACAATTCCAAACAACTCACTAAACTACCACCCAACTAAACAAATAATAAAATTAAACACAATACTTTCCATATCAATATTTCTTTCCTCAACATTTTTAATCAAAAAATAACCTTCAAACTCAATAATATAAAATAAATAACTTATA F:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R2_001.fastq.gz Processed 1000000 sequence pairs so far 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 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 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 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 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Processed 108000000 sequence pairs so far Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Processed 111000000 sequence pairs so far Processed 112000000 sequence pairs so far 112706276 reads; of these: 112706276 (100.00%) were paired; of these: 100843206 (89.47%) aligned concordantly 0 times 3046078 (2.70%) aligned concordantly exactly 1 time 8816992 (7.82%) aligned concordantly >1 times 10.53% overall alignment rate 112706276 reads; of these: 112706276 (100.00%) were paired; of these: 100832704 (89.47%) aligned concordantly 0 times 3050336 (2.71%) aligned concordantly exactly 1 time 8823236 (7.83%) aligned concordantly >1 times 10.53% overall alignment rate Processed 112706276 sequences in total Successfully deleted the temporary files Sealice_F1_S20_L002_R1_001.fastq.gz_C_to_T.fastq and Sealice_F1_S20_L002_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 112706276 Number of paired-end alignments with a unique best hit: 9883349 Mapping efficiency: 8.8% Sequence pairs with no alignments under any condition: 98036031 Sequence pairs did not map uniquely: 4786896 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4927716 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4955633 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 534355619 Total methylated C's in CpG context: 2419146 Total methylated C's in CHG context: 1992060 Total methylated C's in CHH context: 9421424 Total methylated C's in Unknown context: 1713666 Total unmethylated C's in CpG context: 79153095 Total unmethylated C's in CHG context: 83267009 Total unmethylated C's in CHH context: 358102885 Total unmethylated C's in Unknown context: 5385442 C methylated in CpG context: 3.0% C methylated in CHG context: 2.3% C methylated in CHH context: 2.6% C methylated in unknown context (CN or CHN): 24.1% Bismark completed in 0d 6h 30m 34s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/caligus/genome/ (absolute path is '/gscratch/srlab/sr320/data/caligus/genome/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/0101b'): /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R1_001.fastq.gz /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R2_001.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!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/0101b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/caligus/genome/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Sealice_F2_S22_L001_R1_001.fastq.gz to Sealice_F2_S22_L001_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file Sealice_F2_S22_L001_R1_001.fastq.gz (82177525 sequences in total) Writing a G -> A converted version of the input file Sealice_F2_S22_L001_R2_001.fastq.gz to Sealice_F2_S22_L001_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file Sealice_F2_S22_L001_R2_001.fastq.gz (82177525 sequences in total) Input files are Sealice_F2_S22_L001_R1_001.fastq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/caligus/genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L001_R1_001.fastq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAAAGATTGGAAGAGTATATGTTTGAATTTTAGTTATTGTATGATTTTGTATGTTGTTTTTTGTTTGAAAAAGGGGGGGGGGGGGGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF:FFF,:FF:F::,,:FFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATTAAATCAAAAAAACATCATATAAAAAAAAAATATAAATCTCAATAATCACCATATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L001_R1_001.fastq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:1:2101:1407:1016_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 ANTTGAATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAAAGATTGGAAGAGTATATGTTTGAATTTTAGTTATTGTATGATTTTGTATGTTGTTTTTTGTTTGAAAAAGGGGGGGGGGGGGGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF:FFF,:FF:F::,,:FFFFFFFFFFFF YT:Z:UP A00177:85:HCW7VDRXX:1:2101:1407:1016_2:N:0:NGTACG/2 141 * 0 0 * * 0 0 TTTCTTATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATTAAATCAAAAAAACATCATATAAAAAAAAAATATAAATCTCAATAATCACCATATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R2_001.fastq.gz Processed 1000000 sequence pairs so far 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 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 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 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 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far 82177525 reads; of these: 82177525 (100.00%) were paired; of these: 76090435 (92.59%) aligned concordantly 0 times 1423320 (1.73%) aligned concordantly exactly 1 time 4663770 (5.68%) aligned concordantly >1 times 7.41% overall alignment rate 82177525 reads; of these: 82177525 (100.00%) were paired; of these: 76114950 (92.62%) aligned concordantly 0 times 1404990 (1.71%) aligned concordantly exactly 1 time 4657585 (5.67%) aligned concordantly >1 times 7.38% overall alignment rate Processed 82177525 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L001_R1_001.fastq.gz_C_to_T.fastq and Sealice_F2_S22_L001_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 82177525 Number of paired-end alignments with a unique best hit: 4815592 Mapping efficiency: 5.9% Sequence pairs with no alignments under any condition: 74812200 Sequence pairs did not map uniquely: 2549733 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2416982 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2398610 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 269443330 Total methylated C's in CpG context: 1442407 Total methylated C's in CHG context: 1137082 Total methylated C's in CHH context: 5281990 Total methylated C's in Unknown context: 1010601 Total unmethylated C's in CpG context: 42169766 Total unmethylated C's in CHG context: 43933031 Total unmethylated C's in CHH context: 175479054 Total unmethylated C's in Unknown context: 2663577 C methylated in CpG context: 3.3% C methylated in CHG context: 2.5% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 27.5% Bismark completed in 0d 4h 11m 5s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/caligus/genome/ (absolute path is '/gscratch/srlab/sr320/data/caligus/genome/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/0101b'): /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R1_001.fastq.gz /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R2_001.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!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/0101b Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/caligus/genome/ chr Cr_scaffold0000001 (36897007 bp) chr Cr_scaffold0000002 (35124817 bp) chr Cr_scaffold0000003 (33138466 bp) chr Cr_scaffold0000004 (31456035 bp) chr Cr_scaffold0000005 (30612693 bp) chr Cr_scaffold0000006 (30259679 bp) chr Cr_scaffold0000007 (29872177 bp) chr Cr_scaffold0000008 (27803016 bp) chr Cr_scaffold0000009 (25126635 bp) chr Cr_scaffold0000010 (24815513 bp) chr Cr_scaffold0000011 (35794548 bp) chr Cr_scaffold0000012 (22957860 bp) chr Cr_scaffold0000013 (21502856 bp) chr Cr_scaffold0000014 (21148584 bp) chr Cr_scaffold0000015 (19091682 bp) chr Cr_scaffold0000016 (18525937 bp) chr Cr_scaffold0000017 (17562062 bp) chr Cr_scaffold0000018 (14680182 bp) chr Cr_scaffold0000019 (14290452 bp) chr Cr_scaffold0000020 (8286978 bp) chr Cr_scaffold0000021 (8023048 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Sealice_F2_S22_L002_R1_001.fastq.gz to Sealice_F2_S22_L002_R1_001.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file Sealice_F2_S22_L002_R1_001.fastq.gz (81699034 sequences in total) Writing a G -> A converted version of the input file Sealice_F2_S22_L002_R2_001.fastq.gz to Sealice_F2_S22_L002_R2_001.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file Sealice_F2_S22_L002_R2_001.fastq.gz (81699034 sequences in total) Input files are Sealice_F2_S22_L002_R1_001.fastq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/caligus/genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_L002_R1_001.fastq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGGAGATTGGAAGAGTATATGTTTGAATTTTAGTTATTGTATGATTTTGTATGT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:F YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATATAAATCAAAAAAACATCATATAAAAAAAAAATATAAATCTCAATAATCACCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:FFFF,FFFFFFFFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_L002_R1_001.fastq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00177:85:HCW7VDRXX:2:2101:1099:1016_1:N:0:CGTACG/1 77 * 0 0 * * 0 0 ANATAATTTATAAAAATTTAATTTTTATTTTTTTTAATTTTATTTTAATTTTTTTATTTTTTAAAAATAATATATTAAATTTAATAAATATATTTTAGGAGATTGGAAGAGTATATGTTTGAATTTTAGTTATTGTATGATTTTGTATGT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:F YT:Z:UP A00177:85:HCW7VDRXX:2:2101:1099:1016_2:N:0:CGTACG/2 141 * 0 0 * * 0 0 CCTAAAATATATTTATTAAATTTAATATATTATTTTTAAAAAATAAAAAAATTAAAATAAAATTAAAAAAAATAAAAATTAAATTTTTATAAATTATATAAATCAAAAAAACATCATATAAAAAAAAAATATAAATCTCAATAATCACCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:FFFF,FFFFFFFFFFFFF:FF YT:Z:UP >>> Writing bisulfite mapping results to Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R2_001.fastq.gz Processed 1000000 sequence pairs so far 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 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 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 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 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far 81699034 reads; of these: 81699034 (100.00%) were paired; of these: 75812333 (92.79%) aligned concordantly 0 times 1368686 (1.68%) aligned concordantly exactly 1 time 4518015 (5.53%) aligned concordantly >1 times 7.21% overall alignment rate 81699034 reads; of these: 81699034 (100.00%) were paired; of these: 75788790 (92.77%) aligned concordantly 0 times 1385080 (1.70%) aligned concordantly exactly 1 time 4525164 (5.54%) aligned concordantly >1 times 7.23% overall alignment rate Processed 81699034 sequences in total Successfully deleted the temporary files Sealice_F2_S22_L002_R1_001.fastq.gz_C_to_T.fastq and Sealice_F2_S22_L002_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 81699034 Number of paired-end alignments with a unique best hit: 4675527 Mapping efficiency: 5.7% Sequence pairs with no alignments under any condition: 74543184 Sequence pairs did not map uniquely: 2480323 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2346837 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2328690 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 261577090 Total methylated C's in CpG context: 1398442 Total methylated C's in CHG context: 1106576 Total methylated C's in CHH context: 5115414 Total methylated C's in Unknown context: 974335 Total unmethylated C's in CpG context: 40963331 Total unmethylated C's in CHG context: 42673164 Total unmethylated C's in CHH context: 170320163 Total unmethylated C's in Unknown context: 2569263 C methylated in CpG context: 3.3% C methylated in CHG context: 2.5% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 27.5% Bismark completed in 0d 4h 7m 35s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.bam: 10187887 Total number duplicated alignments removed: 2487734 (24.42%) Duplicated alignments were found at: 1695976 different position(s) Total count of deduplicated leftover sequences: 7700153 (75.58% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Cr_scaffold0000001 LN:36897007 skipping header line: @SQ SN:Cr_scaffold0000002 LN:35124817 skipping header line: @SQ SN:Cr_scaffold0000003 LN:33138466 skipping header line: @SQ SN:Cr_scaffold0000004 LN:31456035 skipping header line: @SQ SN:Cr_scaffold0000005 LN:30612693 skipping header line: @SQ SN:Cr_scaffold0000006 LN:30259679 skipping header line: @SQ SN:Cr_scaffold0000007 LN:29872177 skipping header line: @SQ SN:Cr_scaffold0000008 LN:27803016 skipping header line: @SQ SN:Cr_scaffold0000009 LN:25126635 skipping header line: @SQ SN:Cr_scaffold0000010 LN:24815513 skipping header line: @SQ SN:Cr_scaffold0000011 LN:35794548 skipping header line: @SQ SN:Cr_scaffold0000012 LN:22957860 skipping header line: @SQ SN:Cr_scaffold0000013 LN:21502856 skipping header line: @SQ SN:Cr_scaffold0000014 LN:21148584 skipping header line: @SQ SN:Cr_scaffold0000015 LN:19091682 skipping header line: @SQ SN:Cr_scaffold0000016 LN:18525937 skipping header line: @SQ SN:Cr_scaffold0000017 LN:17562062 skipping header line: @SQ SN:Cr_scaffold0000018 LN:14680182 skipping header line: @SQ SN:Cr_scaffold0000019 LN:14290452 skipping header line: @SQ SN:Cr_scaffold0000020 LN:8286978 skipping header line: @SQ SN:Cr_scaffold0000021 LN:8023048 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/caligus/genome/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R1_001.fastq.gz -2 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R2_001.fastq.gz" Processing paired-end Bismark output file(s) (SAM format): Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.bam: 9883349 Total number duplicated alignments removed: 2326847 (23.54%) Duplicated alignments were found at: 1600864 different position(s) Total count of deduplicated leftover sequences: 7556502 (76.46% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Cr_scaffold0000001 LN:36897007 skipping header line: @SQ SN:Cr_scaffold0000002 LN:35124817 skipping header line: @SQ SN:Cr_scaffold0000003 LN:33138466 skipping header line: @SQ SN:Cr_scaffold0000004 LN:31456035 skipping header line: @SQ SN:Cr_scaffold0000005 LN:30612693 skipping header line: @SQ SN:Cr_scaffold0000006 LN:30259679 skipping header line: @SQ SN:Cr_scaffold0000007 LN:29872177 skipping header line: @SQ SN:Cr_scaffold0000008 LN:27803016 skipping header line: @SQ SN:Cr_scaffold0000009 LN:25126635 skipping header line: @SQ SN:Cr_scaffold0000010 LN:24815513 skipping header line: @SQ SN:Cr_scaffold0000011 LN:35794548 skipping header line: @SQ SN:Cr_scaffold0000012 LN:22957860 skipping header line: @SQ SN:Cr_scaffold0000013 LN:21502856 skipping header line: @SQ SN:Cr_scaffold0000014 LN:21148584 skipping header line: @SQ SN:Cr_scaffold0000015 LN:19091682 skipping header line: @SQ SN:Cr_scaffold0000016 LN:18525937 skipping header line: @SQ SN:Cr_scaffold0000017 LN:17562062 skipping header line: @SQ SN:Cr_scaffold0000018 LN:14680182 skipping header line: @SQ SN:Cr_scaffold0000019 LN:14290452 skipping header line: @SQ SN:Cr_scaffold0000020 LN:8286978 skipping header line: @SQ SN:Cr_scaffold0000021 LN:8023048 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/caligus/genome/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R1_001.fastq.gz -2 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R2_001.fastq.gz" Processing paired-end Bismark output file(s) (SAM format): Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.bam: 4815592 Total number duplicated alignments removed: 792982 (16.47%) Duplicated alignments were found at: 570414 different position(s) Total count of deduplicated leftover sequences: 4022610 (83.53% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Cr_scaffold0000001 LN:36897007 skipping header line: @SQ SN:Cr_scaffold0000002 LN:35124817 skipping header line: @SQ SN:Cr_scaffold0000003 LN:33138466 skipping header line: @SQ SN:Cr_scaffold0000004 LN:31456035 skipping header line: @SQ SN:Cr_scaffold0000005 LN:30612693 skipping header line: @SQ SN:Cr_scaffold0000006 LN:30259679 skipping header line: @SQ SN:Cr_scaffold0000007 LN:29872177 skipping header line: @SQ SN:Cr_scaffold0000008 LN:27803016 skipping header line: @SQ SN:Cr_scaffold0000009 LN:25126635 skipping header line: @SQ SN:Cr_scaffold0000010 LN:24815513 skipping header line: @SQ SN:Cr_scaffold0000011 LN:35794548 skipping header line: @SQ SN:Cr_scaffold0000012 LN:22957860 skipping header line: @SQ SN:Cr_scaffold0000013 LN:21502856 skipping header line: @SQ SN:Cr_scaffold0000014 LN:21148584 skipping header line: @SQ SN:Cr_scaffold0000015 LN:19091682 skipping header line: @SQ SN:Cr_scaffold0000016 LN:18525937 skipping header line: @SQ SN:Cr_scaffold0000017 LN:17562062 skipping header line: @SQ SN:Cr_scaffold0000018 LN:14680182 skipping header line: @SQ SN:Cr_scaffold0000019 LN:14290452 skipping header line: @SQ SN:Cr_scaffold0000020 LN:8286978 skipping header line: @SQ SN:Cr_scaffold0000021 LN:8023048 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/caligus/genome/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R1_001.fastq.gz -2 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R2_001.fastq.gz" Processing paired-end Bismark output file(s) (SAM format): Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.bam: 4675527 Total number duplicated alignments removed: 731237 (15.64%) Duplicated alignments were found at: 528737 different position(s) Total count of deduplicated leftover sequences: 3944290 (84.36% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Cr_scaffold0000001 LN:36897007 skipping header line: @SQ SN:Cr_scaffold0000002 LN:35124817 skipping header line: @SQ SN:Cr_scaffold0000003 LN:33138466 skipping header line: @SQ SN:Cr_scaffold0000004 LN:31456035 skipping header line: @SQ SN:Cr_scaffold0000005 LN:30612693 skipping header line: @SQ SN:Cr_scaffold0000006 LN:30259679 skipping header line: @SQ SN:Cr_scaffold0000007 LN:29872177 skipping header line: @SQ SN:Cr_scaffold0000008 LN:27803016 skipping header line: @SQ SN:Cr_scaffold0000009 LN:25126635 skipping header line: @SQ SN:Cr_scaffold0000010 LN:24815513 skipping header line: @SQ SN:Cr_scaffold0000011 LN:35794548 skipping header line: @SQ SN:Cr_scaffold0000012 LN:22957860 skipping header line: @SQ SN:Cr_scaffold0000013 LN:21502856 skipping header line: @SQ SN:Cr_scaffold0000014 LN:21148584 skipping header line: @SQ SN:Cr_scaffold0000015 LN:19091682 skipping header line: @SQ SN:Cr_scaffold0000016 LN:18525937 skipping header line: @SQ SN:Cr_scaffold0000017 LN:17562062 skipping header line: @SQ SN:Cr_scaffold0000018 LN:14680182 skipping header line: @SQ SN:Cr_scaffold0000019 LN:14290452 skipping header line: @SQ SN:Cr_scaffold0000020 LN:8286978 skipping header line: @SQ SN:Cr_scaffold0000021 LN:8023048 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/caligus/genome/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R1_001.fastq.gz -2 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R2_001.fastq.gz" *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/scrubbed/sr320/0101b') Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '75%'. Temporary directory used for sorting is the output directory Checking file >>Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Cr_scaffold0000001 LN:36897007 skipping SAM header line: @SQ SN:Cr_scaffold0000002 LN:35124817 skipping SAM header line: @SQ SN:Cr_scaffold0000003 LN:33138466 skipping SAM header line: @SQ SN:Cr_scaffold0000004 LN:31456035 skipping SAM header line: @SQ SN:Cr_scaffold0000005 LN:30612693 skipping SAM header line: @SQ SN:Cr_scaffold0000006 LN:30259679 skipping SAM header line: @SQ SN:Cr_scaffold0000007 LN:29872177 skipping SAM header line: @SQ SN:Cr_scaffold0000008 LN:27803016 skipping SAM header line: @SQ SN:Cr_scaffold0000009 LN:25126635 skipping SAM header line: @SQ SN:Cr_scaffold0000010 LN:24815513 skipping SAM header line: @SQ SN:Cr_scaffold0000011 LN:35794548 skipping SAM header line: @SQ SN:Cr_scaffold0000012 LN:22957860 skipping SAM header line: @SQ SN:Cr_scaffold0000013 LN:21502856 skipping SAM header line: @SQ SN:Cr_scaffold0000014 LN:21148584 skipping SAM header line: @SQ SN:Cr_scaffold0000015 LN:19091682 skipping SAM header line: @SQ SN:Cr_scaffold0000016 LN:18525937 skipping SAM header line: @SQ SN:Cr_scaffold0000017 LN:17562062 skipping SAM header line: @SQ SN:Cr_scaffold0000018 LN:14680182 skipping SAM header line: @SQ SN:Cr_scaffold0000019 LN:14290452 skipping SAM header line: @SQ SN:Cr_scaffold0000020 LN:8286978 skipping SAM header line: @SQ SN:Cr_scaffold0000021 LN:8023048 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/caligus/genome/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R1_001.fastq.gz -2 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R2_001.fastq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 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Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.1 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.2 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.3 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.4 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.5 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.6 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.7 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.8 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.9 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.10 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.11 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.12 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.13 Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7700153 lines in total Total number of methylation call strings processed: 15400306 Final Cytosine Methylation Report ================================= Total number of C's analysed: 269762284 Total methylated C's in CpG context: 1020695 Total methylated C's in CHG context: 914371 Total methylated C's in CHH context: 4308882 Total C to T conversions in CpG context: 39679136 Total C to T conversions in CHG context: 41823120 Total C to T conversions in CHH context: 182016080 C methylated in CpG context: 2.5% C methylated in CHG context: 2.1% C methylated in CHH context: 2.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt CpG_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt CHG_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt CHG_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt CHH_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt CHH_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/0101b/CpG_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0101b/CpG_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Cr_scaffold0000001 LN:36897007 skipping SAM header line: @SQ SN:Cr_scaffold0000002 LN:35124817 skipping SAM header line: @SQ SN:Cr_scaffold0000003 LN:33138466 skipping SAM header line: @SQ SN:Cr_scaffold0000004 LN:31456035 skipping SAM header line: @SQ SN:Cr_scaffold0000005 LN:30612693 skipping SAM header line: @SQ SN:Cr_scaffold0000006 LN:30259679 skipping SAM header line: @SQ SN:Cr_scaffold0000007 LN:29872177 skipping SAM header line: @SQ SN:Cr_scaffold0000008 LN:27803016 skipping SAM header line: @SQ SN:Cr_scaffold0000009 LN:25126635 skipping SAM header line: @SQ SN:Cr_scaffold0000010 LN:24815513 skipping SAM header line: @SQ SN:Cr_scaffold0000011 LN:35794548 skipping SAM header line: @SQ SN:Cr_scaffold0000012 LN:22957860 skipping SAM header line: @SQ SN:Cr_scaffold0000013 LN:21502856 skipping SAM header line: @SQ SN:Cr_scaffold0000014 LN:21148584 skipping SAM header line: @SQ SN:Cr_scaffold0000015 LN:19091682 skipping SAM header line: @SQ SN:Cr_scaffold0000016 LN:18525937 skipping SAM header line: @SQ SN:Cr_scaffold0000017 LN:17562062 skipping SAM header line: @SQ SN:Cr_scaffold0000018 LN:14680182 skipping SAM header line: @SQ SN:Cr_scaffold0000019 LN:14290452 skipping SAM header line: @SQ SN:Cr_scaffold0000020 LN:8286978 skipping SAM header line: @SQ SN:Cr_scaffold0000021 LN:8023048 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/caligus/genome/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R1_001.fastq.gz -2 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R2_001.fastq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 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Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.1 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.2 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.3 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.4 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.5 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.6 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.7 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.8 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.9 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.10 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.11 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.12 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.13 Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7556502 lines in total Total number of methylation call strings processed: 15113004 Final Cytosine Methylation Report ================================= Total number of C's analysed: 264271058 Total methylated C's in CpG context: 1000643 Total methylated C's in CHG context: 894871 Total methylated C's in CHH context: 4213533 Total C to T conversions in CpG context: 38892968 Total C to T conversions in CHG context: 41001021 Total C to T conversions in CHH context: 178268022 C methylated in CpG context: 2.5% C methylated in CHG context: 2.1% C methylated in CHH context: 2.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt CpG_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt CHG_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt CHG_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt CHH_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt CHH_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/0101b/CpG_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0101b/CpG_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Cr_scaffold0000001 LN:36897007 skipping SAM header line: @SQ SN:Cr_scaffold0000002 LN:35124817 skipping SAM header line: @SQ SN:Cr_scaffold0000003 LN:33138466 skipping SAM header line: @SQ SN:Cr_scaffold0000004 LN:31456035 skipping SAM header line: @SQ SN:Cr_scaffold0000005 LN:30612693 skipping SAM header line: @SQ SN:Cr_scaffold0000006 LN:30259679 skipping SAM header line: @SQ SN:Cr_scaffold0000007 LN:29872177 skipping SAM header line: @SQ SN:Cr_scaffold0000008 LN:27803016 skipping SAM header line: @SQ SN:Cr_scaffold0000009 LN:25126635 skipping SAM header line: @SQ SN:Cr_scaffold0000010 LN:24815513 skipping SAM header line: @SQ SN:Cr_scaffold0000011 LN:35794548 skipping SAM header line: @SQ SN:Cr_scaffold0000012 LN:22957860 skipping SAM header line: @SQ SN:Cr_scaffold0000013 LN:21502856 skipping SAM header line: @SQ SN:Cr_scaffold0000014 LN:21148584 skipping SAM header line: @SQ SN:Cr_scaffold0000015 LN:19091682 skipping SAM header line: @SQ SN:Cr_scaffold0000016 LN:18525937 skipping SAM header line: @SQ SN:Cr_scaffold0000017 LN:17562062 skipping SAM header line: @SQ SN:Cr_scaffold0000018 LN:14680182 skipping SAM header line: @SQ SN:Cr_scaffold0000019 LN:14290452 skipping SAM header line: @SQ SN:Cr_scaffold0000020 LN:8286978 skipping SAM header line: @SQ SN:Cr_scaffold0000021 LN:8023048 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/caligus/genome/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R1_001.fastq.gz -2 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R2_001.fastq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.1 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.2 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.3 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.4 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.5 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.6 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.7 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.8 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.9 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.10 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.11 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.12 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.13 Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4022610 lines in total Total number of methylation call strings processed: 8045220 Final Cytosine Methylation Report ================================= Total number of C's analysed: 137783479 Total methylated C's in CpG context: 623324 Total methylated C's in CHG context: 512711 Total methylated C's in CHH context: 2420387 Total C to T conversions in CpG context: 21511795 Total C to T conversions in CHG context: 22496198 Total C to T conversions in CHH context: 90219064 C methylated in CpG context: 2.8% C methylated in CHG context: 2.2% C methylated in CHH context: 2.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt CpG_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt CHG_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt CHG_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt CHH_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt CHH_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/0101b/CpG_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0101b/CpG_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Cr_scaffold0000001 LN:36897007 skipping SAM header line: @SQ SN:Cr_scaffold0000002 LN:35124817 skipping SAM header line: @SQ SN:Cr_scaffold0000003 LN:33138466 skipping SAM header line: @SQ SN:Cr_scaffold0000004 LN:31456035 skipping SAM header line: @SQ SN:Cr_scaffold0000005 LN:30612693 skipping SAM header line: @SQ SN:Cr_scaffold0000006 LN:30259679 skipping SAM header line: @SQ SN:Cr_scaffold0000007 LN:29872177 skipping SAM header line: @SQ SN:Cr_scaffold0000008 LN:27803016 skipping SAM header line: @SQ SN:Cr_scaffold0000009 LN:25126635 skipping SAM header line: @SQ SN:Cr_scaffold0000010 LN:24815513 skipping SAM header line: @SQ SN:Cr_scaffold0000011 LN:35794548 skipping SAM header line: @SQ SN:Cr_scaffold0000012 LN:22957860 skipping SAM header line: @SQ SN:Cr_scaffold0000013 LN:21502856 skipping SAM header line: @SQ SN:Cr_scaffold0000014 LN:21148584 skipping SAM header line: @SQ SN:Cr_scaffold0000015 LN:19091682 skipping SAM header line: @SQ SN:Cr_scaffold0000016 LN:18525937 skipping SAM header line: @SQ SN:Cr_scaffold0000017 LN:17562062 skipping SAM header line: @SQ SN:Cr_scaffold0000018 LN:14680182 skipping SAM header line: @SQ SN:Cr_scaffold0000019 LN:14290452 skipping SAM header line: @SQ SN:Cr_scaffold0000020 LN:8286978 skipping SAM header line: @SQ SN:Cr_scaffold0000021 LN:8023048 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/caligus/genome/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R1_001.fastq.gz -2 /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R2_001.fastq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.1 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.2 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.3 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.4 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.5 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.6 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.7 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.8 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.9 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.10 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.11 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.12 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.13 Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 3944290 lines in total Total number of methylation call strings processed: 7888580 Final Cytosine Methylation Report ================================= Total number of C's analysed: 134946990 Total methylated C's in CpG context: 608561 Total methylated C's in CHG context: 501154 Total methylated C's in CHH context: 2355542 Total C to T conversions in CpG context: 21084295 Total C to T conversions in CHG context: 22047792 Total C to T conversions in CHH context: 88349646 C methylated in CpG context: 2.8% C methylated in CHG context: 2.2% C methylated in CHH context: 2.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 150 Maximum read length of Read 2: 150 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt CpG_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt CHG_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt CHG_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt CHH_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt CHH_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/0101b/CpG_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0101b/CpG_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 4 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> Sealice_F1_S20_L001_R1_001_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > Sealice_F1_S20_L001_R1_001_bismark_bt2_PE_report.txt < Processing alignment report Sealice_F1_S20_L001_R1_001_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report Sealice_F1_S20_L001_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> Sealice_F1_S20_L002_R1_001_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > Sealice_F1_S20_L002_R1_001_bismark_bt2_PE_report.txt < Processing alignment report Sealice_F1_S20_L002_R1_001_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report Sealice_F1_S20_L002_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> Sealice_F2_S22_L001_R1_001_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > Sealice_F2_S22_L001_R1_001_bismark_bt2_PE_report.txt < Processing alignment report Sealice_F2_S22_L001_R1_001_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report Sealice_F2_S22_L001_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> Sealice_F2_S22_L002_R1_001_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > Sealice_F2_S22_L002_R1_001_bismark_bt2_PE_report.txt < Processing alignment report Sealice_F2_S22_L002_R1_001_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report Sealice_F2_S22_L002_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 4 Bismark BAM file(s)... >> Reading from Bismark report: Sealice_F1_S20_L001_R1_001_bismark_bt2_PE_report.txt >> Reading from Bismark report: Sealice_F1_S20_L002_R1_001_bismark_bt2_PE_report.txt >> Reading from Bismark report: Sealice_F2_S22_L001_R1_001_bismark_bt2_PE_report.txt >> Reading from Bismark report: Sealice_F2_S22_L002_R1_001_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks...