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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-103_S27_L005_R1_001_val_1.fq.gz to EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-103_S27_L005_R1_001_val_1.fq.gz (20349659 sequences in total) Writing a G -> A converted version of the input file EPI-103_S27_L005_R2_001_val_2.fq.gz to EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-103_S27_L005_R2_001_val_2.fq.gz (20349659 sequences in total) Input files are EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1512:1956_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 NGTTTATATGTATGTATTATATTTGTGTAGGTATTGTATTTGATAAGGAT #<<>> Writing bisulfite mapping results to EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2303:16672:27349_1:N:0:ATCACG PGA_scaffold9__45_contigs__length_38581958 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far 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 20349659 reads; of these: 20349659 (100.00%) were paired; of these: 13027775 (64.02%) aligned concordantly 0 times 3373694 (16.58%) aligned concordantly exactly 1 time 3948190 (19.40%) aligned concordantly >1 times 35.98% overall alignment rate 20349659 reads; of these: 20349659 (100.00%) were paired; of these: 13093446 (64.34%) aligned concordantly 0 times 3361315 (16.52%) aligned concordantly exactly 1 time 3894898 (19.14%) aligned concordantly >1 times 35.66% overall alignment rate Processed 20349659 sequences in total Successfully deleted the temporary files EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 20349659 Number of paired-end alignments with a unique best hit: 9095592 Mapping efficiency: 44.7% Sequence pairs with no alignments under any condition: 9572011 Sequence pairs did not map uniquely: 1682056 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4509438 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4586153 ((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: 289949317 Total methylated C's in CpG context: 9619421 Total methylated C's in CHG context: 1310642 Total methylated C's in CHH context: 2350411 Total methylated C's in Unknown context: 40612 Total unmethylated C's in CpG context: 31065297 Total unmethylated C's in CHG context: 59905410 Total unmethylated C's in CHH context: 185698136 Total unmethylated C's in Unknown context: 609374 C methylated in CpG context: 23.6% C methylated in CHG context: 2.1% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.2% Bismark completed in 0d 1h 25m 56s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-104_S28_L005_R1_001_val_1.fq.gz to EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-104_S28_L005_R1_001_val_1.fq.gz (30015261 sequences in total) Writing a G -> A converted version of the input file EPI-104_S28_L005_R2_001_val_2.fq.gz to EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-104_S28_L005_R2_001_val_2.fq.gz (30015261 sequences in total) Input files are EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1112:1988_1:N:0:CGATGT/1 99 PGA_scaffold5__109_contigs__length_67248332_CT_converted 17340906 1 101M = 17341304 497 NGGTGGTAGTTATTAAGTATGTATATGTATTAAAAATTGAAATGAAAAATTATTTTATTAGTTTTTGAAATATTTTGGTATTATATTTAGAGGTGTTTGTG #<>> Writing bisulfite mapping results to EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.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 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1202:6821:3657_1:N:0:CGATGT PGA_scaffold9__45_contigs__length_38581958 2 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 30015261 reads; of these: 30015261 (100.00%) were paired; of these: 18888567 (62.93%) aligned concordantly 0 times 5102104 (17.00%) aligned concordantly exactly 1 time 6024590 (20.07%) aligned concordantly >1 times 37.07% overall alignment rate 30015261 reads; of these: 30015261 (100.00%) were paired; of these: 18948145 (63.13%) aligned concordantly 0 times 5093125 (16.97%) aligned concordantly exactly 1 time 5973991 (19.90%) aligned concordantly >1 times 36.87% overall alignment rate Processed 30015261 sequences in total Successfully deleted the temporary files EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 30015261 Number of paired-end alignments with a unique best hit: 13633936 Mapping efficiency: 45.4% Sequence pairs with no alignments under any condition: 13665400 Sequence pairs did not map uniquely: 2715925 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6781130 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6852805 ((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: 418448650 Total methylated C's in CpG context: 15436769 Total methylated C's in CHG context: 2036052 Total methylated C's in CHH context: 3597610 Total methylated C's in Unknown context: 67853 Total unmethylated C's in CpG context: 41191940 Total unmethylated C's in CHG context: 85561381 Total unmethylated C's in CHH context: 270624898 Total unmethylated C's in Unknown context: 900361 C methylated in CpG context: 27.3% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 7.0% Bismark completed in 0d 2h 7m 52s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-111_S29_L005_R1_001_val_1.fq.gz to EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-111_S29_L005_R1_001_val_1.fq.gz (27014996 sequences in total) Writing a G -> A converted version of the input file EPI-111_S29_L005_R2_001_val_2.fq.gz to EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-111_S29_L005_R2_001_val_2.fq.gz (27014996 sequences in total) Input files are EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1222:1965_1:N:0:TTAGGC/1 99 PGA_scaffold2__36_contigs__length_69596280_CT_converted 52423574 6 101M = 52423755 280 NTGATGAGTGATTTATAATGTTTTGTAGGTTTATTAAAAGATTGTGTTTGTGTTTGTAATTTTTTTGATATATTGTTAATTAAAGTTGGGATGGTTGGATT #<>> Writing bisulfite mapping results to EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2305:8726:65045_1:N:0:TTAGGC PGA_scaffold14__91_contigs__length_45393038 2 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 27014996 reads; of these: 27014996 (100.00%) were paired; of these: 16931638 (62.67%) aligned concordantly 0 times 4662317 (17.26%) aligned concordantly exactly 1 time 5421041 (20.07%) aligned concordantly >1 times 37.33% overall alignment rate 27014996 reads; of these: 27014996 (100.00%) were paired; of these: 17004362 (62.94%) aligned concordantly 0 times 4645643 (17.20%) aligned concordantly exactly 1 time 5364991 (19.86%) aligned concordantly >1 times 37.06% overall alignment rate Processed 27014996 sequences in total Successfully deleted the temporary files EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27014996 Number of paired-end alignments with a unique best hit: 12312883 Mapping efficiency: 45.6% Sequence pairs with no alignments under any condition: 12235438 Sequence pairs did not map uniquely: 2466675 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6118719 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6194163 ((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: 377453061 Total methylated C's in CpG context: 13097257 Total methylated C's in CHG context: 1893893 Total methylated C's in CHH context: 2999476 Total methylated C's in Unknown context: 59372 Total unmethylated C's in CpG context: 39327878 Total unmethylated C's in CHG context: 76742866 Total unmethylated C's in CHH context: 243391691 Total unmethylated C's in Unknown context: 784343 C methylated in CpG context: 25.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 7.0% Bismark completed in 0d 1h 55m 54s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-113_S30_L005_R1_001_val_1.fq.gz to EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-113_S30_L005_R1_001_val_1.fq.gz (26302191 sequences in total) Writing a G -> A converted version of the input file EPI-113_S30_L005_R2_001_val_2.fq.gz to EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-113_S30_L005_R2_001_val_2.fq.gz (26302191 sequences in total) Input files are EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1442:1956_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 NTAGTATTTTTATTAGAAGAATTAGAAATATTAGTAATAGTAAATTATTAGGTAGTGATAATATTGTAAATGAGTAATTAAAGTATTTATTATATGTGATG #>> Writing bisulfite mapping results to EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16931:96627_1:N:0:TGACCA PGA_scaffold13__52_contigs__length_44396874 44396777 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 26302191 reads; of these: 26302191 (100.00%) were paired; of these: 17013134 (64.68%) aligned concordantly 0 times 4367646 (16.61%) aligned concordantly exactly 1 time 4921411 (18.71%) aligned concordantly >1 times 35.32% overall alignment rate 26302191 reads; of these: 26302191 (100.00%) were paired; of these: 16935818 (64.39%) aligned concordantly 0 times 4415733 (16.79%) aligned concordantly exactly 1 time 4950640 (18.82%) aligned concordantly >1 times 35.61% overall alignment rate Processed 26302191 sequences in total Successfully deleted the temporary files EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 26302191 Number of paired-end alignments with a unique best hit: 11581686 Mapping efficiency: 44.0% Sequence pairs with no alignments under any condition: 12489960 Sequence pairs did not map uniquely: 2230545 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5744513 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5837172 ((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: 359357698 Total methylated C's in CpG context: 12471829 Total methylated C's in CHG context: 1771590 Total methylated C's in CHH context: 2827755 Total methylated C's in Unknown context: 53715 Total unmethylated C's in CpG context: 37593518 Total unmethylated C's in CHG context: 73195958 Total unmethylated C's in CHH context: 231497048 Total unmethylated C's in Unknown context: 768555 C methylated in CpG context: 24.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.5% Bismark completed in 0d 1h 48m 52s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-119_S31_L005_R1_001_val_1.fq.gz to EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-119_S31_L005_R1_001_val_1.fq.gz (28905983 sequences in total) Writing a G -> A converted version of the input file EPI-119_S31_L005_R2_001_val_2.fq.gz to EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-119_S31_L005_R2_001_val_2.fq.gz (28905983 sequences in total) Input files are EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1132:1973_1:N:0:ACAGTG/1 99 PGA_scaffold12__71_contigs__length_50438331_CT_converted 4017483 2 93M = 4017483 -93 NTGGTGAAAATTTTGAAAATTGTTTAATAATGGTGTAAAATATTAATTTATATATTATTTTAGTAATTAGGGTGAAATATTTTGAAAGTAAGA #<>> Writing bisulfite mapping results to EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2302:14681:37197_1:N:0:ACAGTG PGA_scaffold16__33_contigs__length_31980953 2 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 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1304:7949:12013_1:N:0:ACAGTG PGA_scaffold16__33_contigs__length_31980953 2 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1215:10856:17476_1:N:0:ACAGTG PGA_scaffold16__33_contigs__length_31980953 2 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 28905983 reads; of these: 28905983 (100.00%) were paired; of these: 19154447 (66.26%) aligned concordantly 0 times 4636303 (16.04%) aligned concordantly exactly 1 time 5115233 (17.70%) aligned concordantly >1 times 33.74% overall alignment rate 28905983 reads; of these: 28905983 (100.00%) were paired; of these: 19005598 (65.75%) aligned concordantly 0 times 4722302 (16.34%) aligned concordantly exactly 1 time 5178083 (17.91%) aligned concordantly >1 times 34.25% overall alignment rate Processed 28905983 sequences in total Successfully deleted the temporary files EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28905983 Number of paired-end alignments with a unique best hit: 12331889 Mapping efficiency: 42.7% Sequence pairs with no alignments under any condition: 14292877 Sequence pairs did not map uniquely: 2281217 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6078960 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6252926 ((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: 389840146 Total methylated C's in CpG context: 12477704 Total methylated C's in CHG context: 1827358 Total methylated C's in CHH context: 3035063 Total methylated C's in Unknown context: 49011 Total unmethylated C's in CpG context: 45041606 Total unmethylated C's in CHG context: 80081549 Total unmethylated C's in CHH context: 247376866 Total unmethylated C's in Unknown context: 795814 C methylated in CpG context: 21.7% C methylated in CHG context: 2.2% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 5.8% Bismark completed in 0d 1h 58m 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-120_S32_L005_R1_001_val_1.fq.gz to EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-120_S32_L005_R1_001_val_1.fq.gz (24140505 sequences in total) Writing a G -> A converted version of the input file EPI-120_S32_L005_R2_001_val_2.fq.gz to EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-120_S32_L005_R2_001_val_2.fq.gz (24140505 sequences in total) Input files are EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1140:1995_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 NGTATTTGGTTATATTTTAATATTAAATTTTGATTAAAATAGTTGTTGAAAATTGATTAGTATTATTTAGGAAGTATAGAAGTGTTAATATAAAGTTAATT #<>> Writing bisulfite mapping results to EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.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 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2203:1403:16239_1:N:0:GCCAAT PGA_scaffold9__45_contigs__length_38581958 2 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2110:13197:92900_1:N:0:GCCAAT PGA_scaffold9__45_contigs__length_38581958 3 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2102:12972:86705_1:N:0:GCCAAT PGA_scaffold9__45_contigs__length_38581958 2 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 24140505 reads; of these: 24140505 (100.00%) were paired; of these: 15252082 (63.18%) aligned concordantly 0 times 4174115 (17.29%) aligned concordantly exactly 1 time 4714308 (19.53%) aligned concordantly >1 times 36.82% overall alignment rate 24140505 reads; of these: 24140505 (100.00%) were paired; of these: 15202444 (62.97%) aligned concordantly 0 times 4175808 (17.30%) aligned concordantly exactly 1 time 4762253 (19.73%) aligned concordantly >1 times 37.03% overall alignment rate Processed 24140505 sequences in total Successfully deleted the temporary files EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24140505 Number of paired-end alignments with a unique best hit: 11050083 Mapping efficiency: 45.8% Sequence pairs with no alignments under any condition: 10973461 Sequence pairs did not map uniquely: 2116961 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5486119 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5563961 ((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: 343610405 Total methylated C's in CpG context: 11964980 Total methylated C's in CHG context: 1672574 Total methylated C's in CHH context: 2746920 Total methylated C's in Unknown context: 46814 Total unmethylated C's in CpG context: 35958013 Total unmethylated C's in CHG context: 69824544 Total unmethylated C's in CHH context: 221443374 Total unmethylated C's in Unknown context: 719473 C methylated in CpG context: 25.0% C methylated in CHG context: 2.3% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.1% Bismark completed in 0d 1h 46m 9s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-127_S33_L005_R1_001_val_1.fq.gz to EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-127_S33_L005_R1_001_val_1.fq.gz (22262118 sequences in total) Writing a G -> A converted version of the input file EPI-127_S33_L005_R2_001_val_2.fq.gz to EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-127_S33_L005_R2_001_val_2.fq.gz (22262118 sequences in total) Input files are EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1259:1963_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 NTATTTATTTTTATATATTATTAAAAATTTATATTTTTATTATTAAAAATATAAATTTATATATTATTAATAATTTATTTTTATATTTTATTAATAAT #<>> Writing bisulfite mapping results to EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2302:15297:83758_1:N:0:CAGATC PGA_scaffold9__45_contigs__length_38581958 1 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 22262118 reads; of these: 22262118 (100.00%) were paired; of these: 14211965 (63.84%) aligned concordantly 0 times 3770814 (16.94%) aligned concordantly exactly 1 time 4279339 (19.22%) aligned concordantly >1 times 36.16% overall alignment rate 22262118 reads; of these: 22262118 (100.00%) were paired; of these: 14293314 (64.20%) aligned concordantly 0 times 3750672 (16.85%) aligned concordantly exactly 1 time 4218132 (18.95%) aligned concordantly >1 times 35.80% overall alignment rate Processed 22262118 sequences in total Successfully deleted the temporary files EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22262118 Number of paired-end alignments with a unique best hit: 9986595 Mapping efficiency: 44.9% Sequence pairs with no alignments under any condition: 10417464 Sequence pairs did not map uniquely: 1858059 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4954421 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5032173 ((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: 314010295 Total methylated C's in CpG context: 11042968 Total methylated C's in CHG context: 1520028 Total methylated C's in CHH context: 2541364 Total methylated C's in Unknown context: 47519 Total unmethylated C's in CpG context: 33055152 Total unmethylated C's in CHG context: 64128787 Total unmethylated C's in CHH context: 201721996 Total unmethylated C's in Unknown context: 647317 C methylated in CpG context: 25.0% C methylated in CHG context: 2.3% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.8% Bismark completed in 0d 1h 35m 27s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-128_S34_L005_R1_001_val_1.fq.gz to EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-128_S34_L005_R1_001_val_1.fq.gz (24557803 sequences in total) Writing a G -> A converted version of the input file EPI-128_S34_L005_R2_001_val_2.fq.gz to EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-128_S34_L005_R2_001_val_2.fq.gz (24557803 sequences in total) Input files are EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1617:1971_1:N:0:ACTTGA/1 99 PGA_scaffold7__69_contigs__length_43120122_CT_converted 39044038 2 98M = 39044221 281 NGAGATTATTTAATATAGATATGTGTTTAAGGTTTTGGTAGATATTGTTAATTATGATTATTGAGGTTATTTAATATAGATATGTTTTAAAGGTTTGG #<<>> Writing bisulfite mapping results to EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.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 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2107:9857:95864_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 2 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 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1116:4355:21006_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 2 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far 24557803 reads; of these: 24557803 (100.00%) were paired; of these: 15638441 (63.68%) aligned concordantly 0 times 4202494 (17.11%) aligned concordantly exactly 1 time 4716868 (19.21%) aligned concordantly >1 times 36.32% overall alignment rate 24557803 reads; of these: 24557803 (100.00%) were paired; of these: 15716613 (64.00%) aligned concordantly 0 times 4172368 (16.99%) aligned concordantly exactly 1 time 4668822 (19.01%) aligned concordantly >1 times 36.00% overall alignment rate Processed 24557803 sequences in total Successfully deleted the temporary files EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24557803 Number of paired-end alignments with a unique best hit: 11023912 Mapping efficiency: 44.9% Sequence pairs with no alignments under any condition: 11430018 Sequence pairs did not map uniquely: 2103873 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5468345 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5555565 ((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: 342815591 Total methylated C's in CpG context: 12084385 Total methylated C's in CHG context: 1712206 Total methylated C's in CHH context: 2665031 Total methylated C's in Unknown context: 47752 Total unmethylated C's in CpG context: 36262181 Total unmethylated C's in CHG context: 69681804 Total unmethylated C's in CHH context: 220409984 Total unmethylated C's in Unknown context: 723863 C methylated in CpG context: 25.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.2% Bismark completed in 0d 1h 45m 36s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-135_S35_L005_R1_001_val_1.fq.gz to EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-135_S35_L005_R1_001_val_1.fq.gz (28731808 sequences in total) Writing a G -> A converted version of the input file EPI-135_S35_L005_R2_001_val_2.fq.gz to EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-135_S35_L005_R2_001_val_2.fq.gz (28731808 sequences in total) Input files are EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1469:1995_1:N:0:GATCAG/1 99 PGA_scaffold2__36_contigs__length_69596280_CT_converted 52412008 1 97M = 52412014 104 NTGTATTTGTTATATTTTTAAAATAAATTAAAATTTTAATTATTTGTTTATTTTGTTTTTTTGGAATTTTGAGTGTATATGTATTATATAATTTATT #<>> Writing bisulfite mapping results to EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.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 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1106:4844:54933_1:N:0:GATCAG PGA_scaffold16__33_contigs__length_31980953 2 Processed 28000000 sequence pairs so far 28731808 reads; of these: 28731808 (100.00%) were paired; of these: 18095326 (62.98%) aligned concordantly 0 times 4833538 (16.82%) aligned concordantly exactly 1 time 5802944 (20.20%) aligned concordantly >1 times 37.02% overall alignment rate 28731808 reads; of these: 28731808 (100.00%) were paired; of these: 18174330 (63.26%) aligned concordantly 0 times 4818195 (16.77%) aligned concordantly exactly 1 time 5739283 (19.98%) aligned concordantly >1 times 36.74% overall alignment rate Processed 28731808 sequences in total Successfully deleted the temporary files EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28731808 Number of paired-end alignments with a unique best hit: 12720631 Mapping efficiency: 44.3% Sequence pairs with no alignments under any condition: 13210078 Sequence pairs did not map uniquely: 2801099 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6307893 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6412737 ((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: 379885177 Total methylated C's in CpG context: 14174074 Total methylated C's in CHG context: 2097825 Total methylated C's in CHH context: 3204273 Total methylated C's in Unknown context: 64166 Total unmethylated C's in CpG context: 39497431 Total unmethylated C's in CHG context: 77915331 Total unmethylated C's in CHH context: 242996243 Total unmethylated C's in Unknown context: 785379 C methylated in CpG context: 26.4% C methylated in CHG context: 2.6% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 7.6% Bismark completed in 0d 1h 59m 27s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-136_S36_L005_R1_001_val_1.fq.gz to EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-136_S36_L005_R1_001_val_1.fq.gz (27792315 sequences in total) Writing a G -> A converted version of the input file EPI-136_S36_L005_R2_001_val_2.fq.gz to EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-136_S36_L005_R2_001_val_2.fq.gz (27792315 sequences in total) Input files are EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1242:1980_1:N:0:TAGCTT/1 99 PGA_scaffold11__79_contigs__length_51449921_CT_converted 30489349 0 100M = 30489366 109 NATGGTTGGATTATTTTATAGTTAAAATATTATGAGGTGTATTGATTGTTTTATTTTGAGATGTTGTGTAGATATTGTTTTAATGGGGTGTAGTGTTTTT #<>> Writing bisulfite mapping results to EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.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 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1205:15387:22738_1:N:0:TAGCTT PGA_scaffold13__52_contigs__length_44396874 44396778 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 27792315 reads; of these: 27792315 (100.00%) were paired; of these: 17566832 (63.21%) aligned concordantly 0 times 4600321 (16.55%) aligned concordantly exactly 1 time 5625162 (20.24%) aligned concordantly >1 times 36.79% overall alignment rate 27792315 reads; of these: 27792315 (100.00%) were paired; of these: 17640819 (63.47%) aligned concordantly 0 times 4583263 (16.49%) aligned concordantly exactly 1 time 5568233 (20.04%) aligned concordantly >1 times 36.53% overall alignment rate Processed 27792315 sequences in total Successfully deleted the temporary files EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27792315 Number of paired-end alignments with a unique best hit: 12229034 Mapping efficiency: 44.0% Sequence pairs with no alignments under any condition: 12912342 Sequence pairs did not map uniquely: 2650939 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6066303 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6162730 ((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: 371098859 Total methylated C's in CpG context: 12526554 Total methylated C's in CHG context: 1883224 Total methylated C's in CHH context: 2923602 Total methylated C's in Unknown context: 54090 Total unmethylated C's in CpG context: 39735089 Total unmethylated C's in CHG context: 76137777 Total unmethylated C's in CHH context: 237892613 Total unmethylated C's in Unknown context: 810936 C methylated in CpG context: 24.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.3% Bismark completed in 0d 1h 55m 19s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-143_S37_L005_R1_001_val_1.fq.gz to EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-143_S37_L005_R1_001_val_1.fq.gz (21160872 sequences in total) Writing a G -> A converted version of the input file EPI-143_S37_L005_R2_001_val_2.fq.gz to EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-143_S37_L005_R2_001_val_2.fq.gz (21160872 sequences in total) Input files are EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1205:1956_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 NGAAGGAAAATGAATTGATAGTATTATAAGGTTTAAATTTGTTATTATTTTTATAATTTGTATTATTTTTATTATTATGTTATATTTTTATAAATAAATTT #<>> Writing bisulfite mapping results to EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.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 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2115:10166:97532_1:N:0:GGCTAC PGA_scaffold9__45_contigs__length_38581958 1 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 21160872 reads; of these: 21160872 (100.00%) were paired; of these: 13649084 (64.50%) aligned concordantly 0 times 3511297 (16.59%) aligned concordantly exactly 1 time 4000491 (18.91%) aligned concordantly >1 times 35.50% overall alignment rate 21160872 reads; of these: 21160872 (100.00%) were paired; of these: 13590247 (64.22%) aligned concordantly 0 times 3523727 (16.65%) aligned concordantly exactly 1 time 4046898 (19.12%) aligned concordantly >1 times 35.78% overall alignment rate Processed 21160872 sequences in total Successfully deleted the temporary files EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 21160872 Number of paired-end alignments with a unique best hit: 9316819 Mapping efficiency: 44.0% Sequence pairs with no alignments under any condition: 10036514 Sequence pairs did not map uniquely: 1807539 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4624000 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4692818 ((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: 288290011 Total methylated C's in CpG context: 10342749 Total methylated C's in CHG context: 1387455 Total methylated C's in CHH context: 2413979 Total methylated C's in Unknown context: 44158 Total unmethylated C's in CpG context: 29588909 Total unmethylated C's in CHG context: 58728884 Total unmethylated C's in CHH context: 185828035 Total unmethylated C's in Unknown context: 610790 C methylated in CpG context: 25.9% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 6.7% Bismark completed in 0d 1h 29m 7s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-145_S38_L005_R1_001_val_1.fq.gz to EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-145_S38_L005_R1_001_val_1.fq.gz (25314513 sequences in total) Writing a G -> A converted version of the input file EPI-145_S38_L005_R2_001_val_2.fq.gz to EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-145_S38_L005_R2_001_val_2.fq.gz (25314513 sequences in total) Input files are EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.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: SL-HBW:624:CAAWVANXX:5:2301:1386:1965_1:N:0:CTTGTA/1 99 PGA_scaffold1__77_contigs__length_89643857_CT_converted 61447290 40 97M = 61447296 105 NTGGGTAAGTAAAGATATAATATTGTAAGTATTATTATGTATATAAGTTTTATATTTTTTTTTTGAGGGTTGAAGTGTTATTATTTTGATATATATT #<>> Writing bisulfite mapping results to EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.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 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2203:7305:92572_1:N:0:CTTGTA PGA_scaffold16__33_contigs__length_31980953 3 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 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1106:12531:67820_1:N:0:CTTGTA PGA_scaffold16__33_contigs__length_31980953 1 Processed 25000000 sequence pairs so far 25314513 reads; of these: 25314513 (100.00%) were paired; of these: 16271826 (64.28%) aligned concordantly 0 times 4267243 (16.86%) aligned concordantly exactly 1 time 4775444 (18.86%) aligned concordantly >1 times 35.72% overall alignment rate 25314513 reads; of these: 25314513 (100.00%) were paired; of these: 16361226 (64.63%) aligned concordantly 0 times 4230313 (16.71%) aligned concordantly exactly 1 time 4722974 (18.66%) aligned concordantly >1 times 35.37% overall alignment rate Processed 25314513 sequences in total Successfully deleted the temporary files EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 25314513 Number of paired-end alignments with a unique best hit: 11191276 Mapping efficiency: 44.2% Sequence pairs with no alignments under any condition: 11992514 Sequence pairs did not map uniquely: 2130723 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5539947 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5651327 ((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: 346932784 Total methylated C's in CpG context: 12322055 Total methylated C's in CHG context: 1693840 Total methylated C's in CHH context: 2773795 Total methylated C's in Unknown context: 48529 Total unmethylated C's in CpG context: 36498527 Total unmethylated C's in CHG context: 70595301 Total unmethylated C's in CHH context: 223049266 Total unmethylated C's in Unknown context: 722709 C methylated in CpG context: 25.2% C methylated in CHG context: 2.3% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.3% Bismark completed in 0d 1h 47m 12s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-41_S38_L005_R1_001_val_1.fq.gz to EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-41_S38_L005_R1_001_val_1.fq.gz (25055317 sequences in total) Writing a G -> A converted version of the input file EPI-41_S38_L005_R2_001_val_2.fq.gz to EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-41_S38_L005_R2_001_val_2.fq.gz (25055317 sequences in total) Input files are EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.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: D00743:144:CAAWNANXX:5:1107:1186:2238_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 GTAGTNTTGGTTGGAATATATATTGTATTGTTATTTGTATTTGGTATATAAGNGGTATNGTNGTTGGTGTTTGGTGTGTAAGTAGTATTGTTGTTGGAGTT BBBBB#>> Writing bisulfite mapping results to EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:5:1203:12890:67154_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:5:2309:19429:51893_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 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 25055317 reads; of these: 25055317 (100.00%) were paired; of these: 16350090 (65.26%) aligned concordantly 0 times 3786709 (15.11%) aligned concordantly exactly 1 time 4918518 (19.63%) aligned concordantly >1 times 34.74% overall alignment rate 25055317 reads; of these: 25055317 (100.00%) were paired; of these: 16269403 (64.93%) aligned concordantly 0 times 3783069 (15.10%) aligned concordantly exactly 1 time 5002845 (19.97%) aligned concordantly >1 times 35.07% overall alignment rate Processed 25055317 sequences in total Successfully deleted the temporary files EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 25055317 Number of paired-end alignments with a unique best hit: 10110534 Mapping efficiency: 40.4% Sequence pairs with no alignments under any condition: 12402840 Sequence pairs did not map uniquely: 2541943 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4993663 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5116869 ((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: 290510503 Total methylated C's in CpG context: 12940226 Total methylated C's in CHG context: 1543391 Total methylated C's in CHH context: 4910085 Total methylated C's in Unknown context: 96039 Total unmethylated C's in CpG context: 28119492 Total unmethylated C's in CHG context: 60698341 Total unmethylated C's in CHH context: 182298968 Total unmethylated C's in Unknown context: 604385 C methylated in CpG context: 31.5% C methylated in CHG context: 2.5% C methylated in CHH context: 2.6% C methylated in unknown context (CN or CHN): 13.7% Bismark completed in 0d 1h 35m 48s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-42_S39_L005_R1_001_val_1.fq.gz to EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-42_S39_L005_R1_001_val_1.fq.gz (29623269 sequences in total) Writing a G -> A converted version of the input file EPI-42_S39_L005_R2_001_val_2.fq.gz to EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-42_S39_L005_R2_001_val_2.fq.gz (29623269 sequences in total) Input files are EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.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: D00743:144:CAAWNANXX:5:1107:1597:2224_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 AGGTANTATGATGTGATGATGGGGTATGATGTGAAGATGGG BBBBB#BBFFFFFFFFFFFFFFFFBFFBFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:5:1107:1597:2224_2:N:0:CGATGT/2 141 * 0 0 * * 0 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNCCT ####################################<#<>> Writing bisulfite mapping results to EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.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 29623269 reads; of these: 29623269 (100.00%) were paired; of these: 18241307 (61.58%) aligned concordantly 0 times 4905564 (16.56%) aligned concordantly exactly 1 time 6476398 (21.86%) aligned concordantly >1 times 38.42% overall alignment rate 29623269 reads; of these: 29623269 (100.00%) were paired; of these: 18159622 (61.30%) aligned concordantly 0 times 4916719 (16.60%) aligned concordantly exactly 1 time 6546928 (22.10%) aligned concordantly >1 times 38.70% overall alignment rate Processed 29623269 sequences in total Successfully deleted the temporary files EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29623269 Number of paired-end alignments with a unique best hit: 13173399 Mapping efficiency: 44.5% Sequence pairs with no alignments under any condition: 13088150 Sequence pairs did not map uniquely: 3361720 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: 6518218 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6655181 ((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: 371864315 Total methylated C's in CpG context: 17401813 Total methylated C's in CHG context: 2029825 Total methylated C's in CHH context: 4531660 Total methylated C's in Unknown context: 68790 Total unmethylated C's in CpG context: 35533244 Total unmethylated C's in CHG context: 78200824 Total unmethylated C's in CHH context: 234166949 Total unmethylated C's in Unknown context: 781521 C methylated in CpG context: 32.9% C methylated in CHG context: 2.5% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 8.1% Bismark completed in 0d 2h 2m 0s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-43_S40_L005_R1_001_val_1.fq.gz to EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-43_S40_L005_R1_001_val_1.fq.gz (22573555 sequences in total) Writing a G -> A converted version of the input file EPI-43_S40_L005_R2_001_val_2.fq.gz to EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-43_S40_L005_R2_001_val_2.fq.gz (22573555 sequences in total) Input files are EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.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: D00743:144:CAAWNANXX:5:1107:1481:2240_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TTTTAATATTAATATATTAAAATATAAAATTTTTATAATTATAATATATATAAATATTATAATATTAATATATTAATATAAAAATTTTATATAATTATAAT BBBBBFF>> Writing bisulfite mapping results to EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.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 22573555 reads; of these: 22573555 (100.00%) were paired; of these: 13873582 (61.46%) aligned concordantly 0 times 3802013 (16.84%) aligned concordantly exactly 1 time 4897960 (21.70%) aligned concordantly >1 times 38.54% overall alignment rate 22573555 reads; of these: 22573555 (100.00%) were paired; of these: 13942903 (61.77%) aligned concordantly 0 times 3795765 (16.82%) aligned concordantly exactly 1 time 4834887 (21.42%) aligned concordantly >1 times 38.23% overall alignment rate Processed 22573555 sequences in total Successfully deleted the temporary files EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22573555 Number of paired-end alignments with a unique best hit: 10112774 Mapping efficiency: 44.8% Sequence pairs with no alignments under any condition: 10003930 Sequence pairs did not map uniquely: 2456851 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: 5003413 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5109361 ((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: 291124282 Total methylated C's in CpG context: 12587981 Total methylated C's in CHG context: 1494744 Total methylated C's in CHH context: 5077384 Total methylated C's in Unknown context: 67963 Total unmethylated C's in CpG context: 28303550 Total unmethylated C's in CHG context: 60291324 Total unmethylated C's in CHH context: 183369299 Total unmethylated C's in Unknown context: 592883 C methylated in CpG context: 30.8% C methylated in CHG context: 2.4% C methylated in CHH context: 2.7% C methylated in unknown context (CN or CHN): 10.3% Bismark completed in 0d 1h 34m 4s ==================== 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/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' 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/sr320/0809-005'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.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/sr320/0809-005 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-44_S41_L005_R1_001_val_1.fq.gz to EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-44_S41_L005_R1_001_val_1.fq.gz (13762658 sequences in total) Writing a G -> A converted version of the input file EPI-44_S41_L005_R2_001_val_2.fq.gz to EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-44_S41_L005_R2_001_val_2.fq.gz (13762658 sequences in total) Input files are EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ 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 EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.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: D00743:144:CAAWNANXX:5:1107:1348:2233_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AATTTNGGTGTATAGTTTAAGTTAGGAAAGTTTTTTTTATTAAATTGTTTTGTTATGTTTAAATAGATATTTTTTTGGTAGTAT BBBBB#/B>> Writing bisulfite mapping results to EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:5:1215:4007:34225_1:N:0:ACTTGA PGA_scaffold9__45_contigs__length_38581958 1 13762658 reads; of these: 13762658 (100.00%) were paired; of these: 8493354 (61.71%) aligned concordantly 0 times 2308211 (16.77%) aligned concordantly exactly 1 time 2961093 (21.52%) aligned concordantly >1 times 38.29% overall alignment rate 13762658 reads; of these: 13762658 (100.00%) were paired; of these: 8468686 (61.53%) aligned concordantly 0 times 2306213 (16.76%) aligned concordantly exactly 1 time 2987759 (21.71%) aligned concordantly >1 times 38.47% overall alignment rate Processed 13762658 sequences in total Successfully deleted the temporary files EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 13762658 Number of paired-end alignments with a unique best hit: 6084805 Mapping efficiency: 44.2% Sequence pairs with no alignments under any condition: 6118468 Sequence pairs did not map uniquely: 1559385 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3020647 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3064157 ((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: 170813493 Total methylated C's in CpG context: 8105964 Total methylated C's in CHG context: 922535 Total methylated C's in CHH context: 2562650 Total methylated C's in Unknown context: 43087 Total unmethylated C's in CpG context: 16050613 Total unmethylated C's in CHG context: 35418280 Total unmethylated C's in CHH context: 107753451 Total unmethylated C's in Unknown context: 349691 C methylated in CpG context: 33.6% C methylated in CHG context: 2.5% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 11.0% Bismark completed in 0d 0h 56m 20s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): EPI-103_S27_L005_R1_001_val_1_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 >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam: 9095591 Total number duplicated alignments removed: 1259755 (13.85%) Duplicated alignments were found at: 632529 different position(s) Total count of deduplicated leftover sequences: 7835836 (86.15% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-104_S28_L005_R1_001_val_1_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 >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam: 13633935 Total number duplicated alignments removed: 2020190 (14.82%) Duplicated alignments were found at: 1117791 different position(s) Total count of deduplicated leftover sequences: 11613745 (85.18% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-111_S29_L005_R1_001_val_1_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 >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam: 12312882 Total number duplicated alignments removed: 1846060 (14.99%) Duplicated alignments were found at: 941145 different position(s) Total count of deduplicated leftover sequences: 10466822 (85.01% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-113_S30_L005_R1_001_val_1_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 >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam: 11581685 Total number duplicated alignments removed: 1726942 (14.91%) Duplicated alignments were found at: 879906 different position(s) Total count of deduplicated leftover sequences: 9854743 (85.09% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-119_S31_L005_R1_001_val_1_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 >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam: 12331886 Total number duplicated alignments removed: 1918064 (15.55%) Duplicated alignments were found at: 946129 different position(s) Total count of deduplicated leftover sequences: 10413822 (84.45% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-120_S32_L005_R1_001_val_1_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 >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam: 11050080 Total number duplicated alignments removed: 1579974 (14.30%) Duplicated alignments were found at: 825606 different position(s) Total count of deduplicated leftover sequences: 9470106 (85.70% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-127_S33_L005_R1_001_val_1_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 >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam: 9986594 Total number duplicated alignments removed: 1536515 (15.39%) Duplicated alignments were found at: 782021 different position(s) Total count of deduplicated leftover sequences: 8450079 (84.61% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-128_S34_L005_R1_001_val_1_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 >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam: 11023910 Total number duplicated alignments removed: 1723786 (15.64%) Duplicated alignments were found at: 865786 different position(s) Total count of deduplicated leftover sequences: 9300124 (84.36% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-135_S35_L005_R1_001_val_1_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 >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam: 12720630 Total number duplicated alignments removed: 2161126 (16.99%) Duplicated alignments were found at: 1085821 different position(s) Total count of deduplicated leftover sequences: 10559504 (83.01% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-136_S36_L005_R1_001_val_1_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 >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam: 12229033 Total number duplicated alignments removed: 1939155 (15.86%) Duplicated alignments were found at: 929619 different position(s) Total count of deduplicated leftover sequences: 10289878 (84.14% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-143_S37_L005_R1_001_val_1_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 >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam: 9316818 Total number duplicated alignments removed: 1420739 (15.25%) Duplicated alignments were found at: 811691 different position(s) Total count of deduplicated leftover sequences: 7896079 (84.75% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-145_S38_L005_R1_001_val_1_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 >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam: 11191274 Total number duplicated alignments removed: 1835341 (16.40%) Duplicated alignments were found at: 997702 different position(s) Total count of deduplicated leftover sequences: 9355933 (83.60% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-41_S38_L005_R1_001_val_1_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 >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam: 10110532 Total number duplicated alignments removed: 3711212 (36.71%) Duplicated alignments were found at: 2206337 different position(s) Total count of deduplicated leftover sequences: 6399320 (63.29% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-42_S39_L005_R1_001_val_1_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 >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam: 13173399 Total number duplicated alignments removed: 4597382 (34.90%) Duplicated alignments were found at: 2730000 different position(s) Total count of deduplicated leftover sequences: 8576017 (65.10% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-43_S40_L005_R1_001_val_1_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 >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam: 10112774 Total number duplicated alignments removed: 3692163 (36.51%) Duplicated alignments were found at: 2223544 different position(s) Total count of deduplicated leftover sequences: 6420611 (63.49% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-44_S41_L005_R1_001_val_1_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 >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam: 6084804 Total number duplicated alignments removed: 2053760 (33.75%) Duplicated alignments were found at: 1305099 different position(s) Total count of deduplicated leftover sequences: 4031044 (66.25% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz" *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file EPI-103_S27_L005_R1_001_val_1_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/sr320/0809-005') 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 >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-103_S27_L005_R1_001_val_1_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_EPI-103_S27_L005_R1_001_val_1_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_EPI-103_S27_L005_R1_001_val_1_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_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-103_S27_L005_R1_001_val_1_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_EPI-103_S27_L005_R1_001_val_1_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_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-103_S27_L005_R1_001_val_1_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_EPI-103_S27_L005_R1_001_val_1_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_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.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 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lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 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: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 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 Processed lines: 7500000 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: 'EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7835836 lines in total Total number of methylation call strings processed: 15671672 Final Cytosine Methylation Report ================================= Total number of C's analysed: 183501406 Total methylated C's in CpG context: 6658001 Total methylated C's in CHG context: 852229 Total methylated C's in CHH context: 1574350 Total C to T conversions in CpG context: 18809270 Total C to T conversions in CHG context: 36884209 Total C to T conversions in CHH context: 118723347 C methylated in CpG context: 26.1% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-103_S27_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-103_S27_L005_R1_001_val_1_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 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-104_S28_L005_R1_001_val_1_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_EPI-104_S28_L005_R1_001_val_1_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_EPI-104_S28_L005_R1_001_val_1_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_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-104_S28_L005_R1_001_val_1_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_EPI-104_S28_L005_R1_001_val_1_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_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-104_S28_L005_R1_001_val_1_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_EPI-104_S28_L005_R1_001_val_1_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_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_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 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.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 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Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11000000 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.. Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Processed lines: 11500000 Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 11613745 lines in total Total number of methylation call strings processed: 23227490 Final Cytosine Methylation Report ================================= Total number of C's analysed: 256681996 Total methylated C's in CpG context: 10137100 Total methylated C's in CHG context: 1260299 Total methylated C's in CHH context: 2323535 Total C to T conversions in CpG context: 24263858 Total C to T conversions in CHG context: 51430750 Total C to T conversions in CHH context: 167266454 C methylated in CpG context: 29.5% C methylated in CHG context: 2.4% C methylated in CHH context: 1.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-104_S28_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-104_S28_L005_R1_001_val_1_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 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-111_S29_L005_R1_001_val_1_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_EPI-111_S29_L005_R1_001_val_1_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_EPI-111_S29_L005_R1_001_val_1_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_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-111_S29_L005_R1_001_val_1_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_EPI-111_S29_L005_R1_001_val_1_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_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-111_S29_L005_R1_001_val_1_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_EPI-111_S29_L005_R1_001_val_1_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_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.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 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10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 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.. Processed lines: 10000000 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.. Merging individual splitting reports into overall report: 'EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10466822 lines in total Total number of methylation call strings processed: 20933644 Final Cytosine Methylation Report ================================= Total number of C's analysed: 231214858 Total methylated C's in CpG context: 8681437 Total methylated C's in CHG context: 1156157 Total methylated C's in CHH context: 1936920 Total C to T conversions in CpG context: 22978618 Total C to T conversions in CHG context: 46067897 Total C to T conversions in CHH context: 150393829 C methylated in CpG context: 27.4% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-111_S29_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-111_S29_L005_R1_001_val_1_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 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-113_S30_L005_R1_001_val_1_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_EPI-113_S30_L005_R1_001_val_1_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_EPI-113_S30_L005_R1_001_val_1_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_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-113_S30_L005_R1_001_val_1_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_EPI-113_S30_L005_R1_001_val_1_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_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-113_S30_L005_R1_001_val_1_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_EPI-113_S30_L005_R1_001_val_1_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_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.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 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lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9000000 Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 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.. Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9854743 lines in total Total number of methylation call strings processed: 19709486 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224084049 Total methylated C's in CpG context: 8423482 Total methylated C's in CHG context: 1104529 Total methylated C's in CHH context: 1867274 Total C to T conversions in CpG context: 22028913 Total C to T conversions in CHG context: 44713152 Total C to T conversions in CHH context: 145946699 C methylated in CpG context: 27.7% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-113_S30_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-113_S30_L005_R1_001_val_1_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 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-119_S31_L005_R1_001_val_1_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_EPI-119_S31_L005_R1_001_val_1_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_EPI-119_S31_L005_R1_001_val_1_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_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-119_S31_L005_R1_001_val_1_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_EPI-119_S31_L005_R1_001_val_1_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_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-119_S31_L005_R1_001_val_1_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_EPI-119_S31_L005_R1_001_val_1_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_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_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 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.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 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child process. Exiting.. Processed lines: 10000000 Processed lines: 10000000 Finished processing child process. Exiting.. Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10413822 lines in total Total number of methylation call strings processed: 20827644 Final Cytosine Methylation Report ================================= Total number of C's analysed: 243953258 Total methylated C's in CpG context: 8558544 Total methylated C's in CHG context: 1135855 Total methylated C's in CHH context: 2017566 Total C to T conversions in CpG context: 25838202 Total C to T conversions in CHG context: 48531203 Total C to T conversions in CHH context: 157871888 C methylated in CpG context: 24.9% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-119_S31_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-119_S31_L005_R1_001_val_1_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 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-120_S32_L005_R1_001_val_1_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_EPI-120_S32_L005_R1_001_val_1_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_EPI-120_S32_L005_R1_001_val_1_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_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-120_S32_L005_R1_001_val_1_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_EPI-120_S32_L005_R1_001_val_1_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_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-120_S32_L005_R1_001_val_1_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_EPI-120_S32_L005_R1_001_val_1_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_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.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 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Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9470106 lines in total Total number of methylation call strings processed: 18940212 Final Cytosine Methylation Report ================================= Total number of C's analysed: 217946429 Total methylated C's in CpG context: 8187042 Total methylated C's in CHG context: 1062536 Total methylated C's in CHH context: 1832611 Total C to T conversions in CpG context: 21761145 Total C to T conversions in CHG context: 43433409 Total C to T conversions in CHH context: 141669686 C methylated in CpG context: 27.3% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-120_S32_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-120_S32_L005_R1_001_val_1_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 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-127_S33_L005_R1_001_val_1_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_EPI-127_S33_L005_R1_001_val_1_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_EPI-127_S33_L005_R1_001_val_1_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_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-127_S33_L005_R1_001_val_1_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_EPI-127_S33_L005_R1_001_val_1_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_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-127_S33_L005_R1_001_val_1_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_EPI-127_S33_L005_R1_001_val_1_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_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_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 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.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 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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: 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 Processed lines: 8000000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Finished processing child process. Exiting.. Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8450079 lines in total Total number of methylation call strings processed: 16900158 Final Cytosine Methylation Report ================================= Total number of C's analysed: 196938082 Total methylated C's in CpG context: 7564205 Total methylated C's in CHG context: 967557 Total methylated C's in CHH context: 1694338 Total C to T conversions in CpG context: 19544907 Total C to T conversions in CHG context: 39233900 Total C to T conversions in CHH context: 127933175 C methylated in CpG context: 27.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-127_S33_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-127_S33_L005_R1_001_val_1_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 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-128_S34_L005_R1_001_val_1_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_EPI-128_S34_L005_R1_001_val_1_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_EPI-128_S34_L005_R1_001_val_1_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_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-128_S34_L005_R1_001_val_1_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_EPI-128_S34_L005_R1_001_val_1_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_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-128_S34_L005_R1_001_val_1_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_EPI-128_S34_L005_R1_001_val_1_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_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.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 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Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 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.. Processed lines: 9000000 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.. Merging individual splitting reports into overall report: 'EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9300124 lines in total Total number of methylation call strings processed: 18600248 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215109906 Total methylated C's in CpG context: 8244675 Total methylated C's in CHG context: 1071477 Total methylated C's in CHH context: 1772832 Total C to T conversions in CpG context: 21307910 Total C to T conversions in CHG context: 42824701 Total C to T conversions in CHH context: 139888311 C methylated in CpG context: 27.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-128_S34_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-128_S34_L005_R1_001_val_1_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 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-135_S35_L005_R1_001_val_1_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_EPI-135_S35_L005_R1_001_val_1_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_EPI-135_S35_L005_R1_001_val_1_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_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-135_S35_L005_R1_001_val_1_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_EPI-135_S35_L005_R1_001_val_1_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_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-135_S35_L005_R1_001_val_1_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_EPI-135_S35_L005_R1_001_val_1_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_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.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 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Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10500000 Now waiting for all child processes to complete Processed lines: 10500000 Processed lines: 10500000 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: 'EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10559504 lines in total Total number of methylation call strings processed: 21119008 Final Cytosine Methylation Report ================================= Total number of C's analysed: 225992948 Total methylated C's in CpG context: 9046557 Total methylated C's in CHG context: 1202237 Total methylated C's in CHH context: 2001278 Total C to T conversions in CpG context: 21842118 Total C to T conversions in CHG context: 45361388 Total C to T conversions in CHH context: 146539370 C methylated in CpG context: 29.3% C methylated in CHG context: 2.6% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-135_S35_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-135_S35_L005_R1_001_val_1_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 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-136_S36_L005_R1_001_val_1_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_EPI-136_S36_L005_R1_001_val_1_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_EPI-136_S36_L005_R1_001_val_1_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_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-136_S36_L005_R1_001_val_1_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_EPI-136_S36_L005_R1_001_val_1_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_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-136_S36_L005_R1_001_val_1_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_EPI-136_S36_L005_R1_001_val_1_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_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_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 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.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 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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.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10289878 lines in total Total number of methylation call strings processed: 20579756 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222520026 Total methylated C's in CpG context: 8205504 Total methylated C's in CHG context: 1105916 Total methylated C's in CHH context: 1849444 Total C to T conversions in CpG context: 22514794 Total C to T conversions in CHG context: 44690621 Total C to T conversions in CHH context: 144153747 C methylated in CpG context: 26.7% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-136_S36_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-136_S36_L005_R1_001_val_1_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 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-143_S37_L005_R1_001_val_1_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_EPI-143_S37_L005_R1_001_val_1_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_EPI-143_S37_L005_R1_001_val_1_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_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-143_S37_L005_R1_001_val_1_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_EPI-143_S37_L005_R1_001_val_1_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_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-143_S37_L005_R1_001_val_1_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_EPI-143_S37_L005_R1_001_val_1_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_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_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 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.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 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Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 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 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.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7896079 lines in total Total number of methylation call strings processed: 15792158 Final Cytosine Methylation Report ================================= Total number of C's analysed: 180013500 Total methylated C's in CpG context: 6934397 Total methylated C's in CHG context: 872844 Total methylated C's in CHH context: 1579087 Total C to T conversions in CpG context: 17647358 Total C to T conversions in CHG context: 35893215 Total C to T conversions in CHH context: 117086599 C methylated in CpG context: 28.2% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-143_S37_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-143_S37_L005_R1_001_val_1_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 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-145_S38_L005_R1_001_val_1_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_EPI-145_S38_L005_R1_001_val_1_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_EPI-145_S38_L005_R1_001_val_1_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_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-145_S38_L005_R1_001_val_1_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_EPI-145_S38_L005_R1_001_val_1_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_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-145_S38_L005_R1_001_val_1_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_EPI-145_S38_L005_R1_001_val_1_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_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_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 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.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: 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Exiting.. Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9355933 lines in total Total number of methylation call strings processed: 18711866 Final Cytosine Methylation Report ================================= Total number of C's analysed: 214985786 Total methylated C's in CpG context: 8245428 Total methylated C's in CHG context: 1047240 Total methylated C's in CHH context: 1811240 Total C to T conversions in CpG context: 21238566 Total C to T conversions in CHG context: 42806098 Total C to T conversions in CHH context: 139837214 C methylated in CpG context: 28.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-145_S38_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-145_S38_L005_R1_001_val_1_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 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-41_S38_L005_R1_001_val_1_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_EPI-41_S38_L005_R1_001_val_1_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_EPI-41_S38_L005_R1_001_val_1_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_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-41_S38_L005_R1_001_val_1_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_EPI-41_S38_L005_R1_001_val_1_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_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-41_S38_L005_R1_001_val_1_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_EPI-41_S38_L005_R1_001_val_1_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_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_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 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.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 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Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 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.. 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.. Merging individual splitting reports into overall report: 'EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6399320 lines in total Total number of methylation call strings processed: 12798640 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128539262 Total methylated C's in CpG context: 5867583 Total methylated C's in CHG context: 687621 Total methylated C's in CHH context: 2454676 Total C to T conversions in CpG context: 11862497 Total C to T conversions in CHG context: 26124666 Total C to T conversions in CHH context: 81542219 C methylated in CpG context: 33.1% C methylated in CHG context: 2.6% C methylated in CHH context: 2.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-41_S38_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-41_S38_L005_R1_001_val_1_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 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-42_S39_L005_R1_001_val_1_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_EPI-42_S39_L005_R1_001_val_1_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_EPI-42_S39_L005_R1_001_val_1_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_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-42_S39_L005_R1_001_val_1_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_EPI-42_S39_L005_R1_001_val_1_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_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-42_S39_L005_R1_001_val_1_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_EPI-42_S39_L005_R1_001_val_1_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_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.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 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Exiting.. Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 8500000 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.. Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 8500000 Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8576017 lines in total Total number of methylation call strings processed: 17152034 Final Cytosine Methylation Report ================================= Total number of C's analysed: 167743909 Total methylated C's in CpG context: 8085260 Total methylated C's in CHG context: 910439 Total methylated C's in CHH context: 2251034 Total C to T conversions in CpG context: 15228220 Total C to T conversions in CHG context: 34537608 Total C to T conversions in CHH context: 106731348 C methylated in CpG context: 34.7% C methylated in CHG context: 2.6% C methylated in CHH context: 2.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-42_S39_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-42_S39_L005_R1_001_val_1_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 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-43_S40_L005_R1_001_val_1_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_EPI-43_S40_L005_R1_001_val_1_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_EPI-43_S40_L005_R1_001_val_1_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_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-43_S40_L005_R1_001_val_1_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_EPI-43_S40_L005_R1_001_val_1_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_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-43_S40_L005_R1_001_val_1_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_EPI-43_S40_L005_R1_001_val_1_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_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.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 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Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Processed lines: 6000000 Processed lines: 6000000 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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6420611 lines in total Total number of methylation call strings processed: 12841222 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128026299 Total methylated C's in CpG context: 5689722 Total methylated C's in CHG context: 671794 Total methylated C's in CHH context: 2537937 Total C to T conversions in CpG context: 11970270 Total C to T conversions in CHG context: 25906277 Total C to T conversions in CHH context: 81250299 C methylated in CpG context: 32.2% C methylated in CHG context: 2.5% C methylated in CHH context: 3.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-43_S40_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-43_S40_L005_R1_001_val_1_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 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-44_S41_L005_R1_001_val_1_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_EPI-44_S41_L005_R1_001_val_1_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_EPI-44_S41_L005_R1_001_val_1_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_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-44_S41_L005_R1_001_val_1_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_EPI-44_S41_L005_R1_001_val_1_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_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-44_S41_L005_R1_001_val_1_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_EPI-44_S41_L005_R1_001_val_1_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_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_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 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_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:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping SAM header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping SAM header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping SAM header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping SAM header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping SAM header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping SAM header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping SAM header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping SAM header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping SAM header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping SAM header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping SAM header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping SAM header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping SAM header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping SAM header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping SAM header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping SAM header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping SAM header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 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/geoduck/v074 -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.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 Finished processing child process. Exiting.. Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. 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.. Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4031044 lines in total Total number of methylation call strings processed: 8062088 Final Cytosine Methylation Report ================================= Total number of C's analysed: 79983322 Total methylated C's in CpG context: 3855731 Total methylated C's in CHG context: 431899 Total methylated C's in CHH context: 1321843 Total C to T conversions in CpG context: 7250942 Total C to T conversions in CHG context: 16319796 Total C to T conversions in CHH context: 50803111 C methylated in CpG context: 34.7% C methylated in CHG context: 2.6% C methylated in CHH context: 2.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 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: 101 Maximum read length of Read 2: 99 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_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-44_S41_L005_R1_001_val_1_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/sr320/0809-005/CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0809-005/CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-44_S41_L005_R1_001_val_1_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 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 16 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-44_S41_L005_R1_001_val_1_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 16 Bismark BAM file(s)... >> Reading from Bismark report: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-44_S41_L005_R1_001_val_1_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... [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... [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... [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...