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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_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/sr320/0807-003 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-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-175_S14_L003_R1_001_val_1.fq.gz to EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-175_S14_L003_R1_001_val_1.fq.gz (24654280 sequences in total) Writing a G -> A converted version of the input file EPI-175_S14_L003_R2_001_val_2.fq.gz to EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-175_S14_L003_R2_001_val_2.fq.gz (24654280 sequences in total) Input files are EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_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-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_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:3:1107:1436:2247_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 AAGAANATGTGTTTGTATGTTGGAAGTTTGTTTAGTGTGG BBBBB#>> Writing bisulfite mapping results to EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1308:2082:73549_1:N:0:ATCACG PGA_scaffold9__45_contigs__length_38581958 1 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 24654280 reads; of these: 24654280 (100.00%) were paired; of these: 16285716 (66.06%) aligned concordantly 0 times 3719776 (15.09%) aligned concordantly exactly 1 time 4648788 (18.86%) aligned concordantly >1 times 33.94% overall alignment rate 24654280 reads; of these: 24654280 (100.00%) were paired; of these: 16219919 (65.79%) aligned concordantly 0 times 3719837 (15.09%) aligned concordantly exactly 1 time 4714524 (19.12%) aligned concordantly >1 times 34.21% overall alignment rate Processed 24654280 sequences in total Successfully deleted the temporary files EPI-175_S14_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-175_S14_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24654280 Number of paired-end alignments with a unique best hit: 10209530 Mapping efficiency: 41.4% Sequence pairs with no alignments under any condition: 12327982 Sequence pairs did not map uniquely: 2116768 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: 5041243 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5168286 ((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: 309993582 Total methylated C's in CpG context: 11855544 Total methylated C's in CHG context: 1437285 Total methylated C's in CHH context: 3685251 Total methylated C's in Unknown context: 57157 Total unmethylated C's in CpG context: 31961048 Total unmethylated C's in CHG context: 65204352 Total unmethylated C's in CHH context: 195850102 Total unmethylated C's in Unknown context: 677780 C methylated in CpG context: 27.1% C methylated in CHG context: 2.2% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 7.8% Bismark completed in 0d 1h 35m 42s ==================== 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_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/sr320/0807-003 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-176_S15_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-176_S15_L003_R1_001_val_1.fq.gz to EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-176_S15_L003_R1_001_val_1.fq.gz (36345555 sequences in total) Writing a G -> A converted version of the input file EPI-176_S15_L003_R2_001_val_2.fq.gz to EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-176_S15_L003_R2_001_val_2.fq.gz (36345555 sequences in total) Input files are EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_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-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_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:3:1107:4405:2246_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 TGTGGNGTAGATGAAGATGTTTGATATGTTGTAGAATATGTAGTTGTAGAGTGTTATTGTGAAGGTGATGTATGTTGTTATTATTGAGAG BBBBB#B>> Writing bisulfite mapping results to EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1102:4573:54620_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1103:17389:25945_1:N:0:CGATGT PGA_scaffold2__36_contigs__length_69596280 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1104:15612:91578_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2201:12506:83456_1:N:0:CGATGT PGA_scaffold8__63_contigs__length_61151155 61151062 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2205:13682:89946_1:N:0:CGATGT PGA_scaffold9__45_contigs__length_38581958 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2109:14625:56631_1:N:0:CGATGT PGA_scaffold8__63_contigs__length_61151155 61151062 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1208:8738:55944_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 2 Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far 36345555 reads; of these: 36345555 (100.00%) were paired; of these: 25118626 (69.11%) aligned concordantly 0 times 5091930 (14.01%) aligned concordantly exactly 1 time 6134999 (16.88%) aligned concordantly >1 times 30.89% overall alignment rate 36345555 reads; of these: 36345555 (100.00%) were paired; of these: 25018491 (68.84%) aligned concordantly 0 times 5092475 (14.01%) aligned concordantly exactly 1 time 6234589 (17.15%) aligned concordantly >1 times 31.16% overall alignment rate Processed 36345555 sequences in total Successfully deleted the temporary files EPI-176_S15_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-176_S15_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 36345555 Number of paired-end alignments with a unique best hit: 13724724 Mapping efficiency: 37.8% Sequence pairs with no alignments under any condition: 19810124 Sequence pairs did not map uniquely: 2810707 Sequence pairs which were discarded because genomic sequence could not be extracted: 7 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6759192 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6965525 ((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: 415508402 Total methylated C's in CpG context: 15449887 Total methylated C's in CHG context: 1795361 Total methylated C's in CHH context: 4293575 Total methylated C's in Unknown context: 73998 Total unmethylated C's in CpG context: 44600919 Total unmethylated C's in CHG context: 86098830 Total unmethylated C's in CHH context: 263269830 Total unmethylated C's in Unknown context: 887032 C methylated in CpG context: 25.7% C methylated in CHG context: 2.0% C methylated in CHH context: 1.6% C methylated in unknown context (CN or CHN): 7.7% Bismark completed in 0d 2h 8m 31s ==================== 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_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/sr320/0807-003 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-181_S16_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-181_S16_L003_R1_001_val_1.fq.gz to EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-181_S16_L003_R1_001_val_1.fq.gz (27212918 sequences in total) Writing a G -> A converted version of the input file EPI-181_S16_L003_R2_001_val_2.fq.gz to EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-181_S16_L003_R2_001_val_2.fq.gz (27212918 sequences in total) Input files are EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_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-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_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:3:1107:3117:2249_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 GTTAGNGTTTAAAATATATGTATATTGAATATGTAGTAATTATATAGATAAAGTTTTATTGGTTATAAAATAGGGATGTTTTTAGTTTTGTTGAGTAT BBBBB#>> Writing bisulfite mapping results to EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1316:13789:41230_1:N:0:TTAGGC PGA_scaffold16__33_contigs__length_31980953 2 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 27212918 reads; of these: 27212918 (100.00%) were paired; of these: 18377954 (67.53%) aligned concordantly 0 times 3966469 (14.58%) aligned concordantly exactly 1 time 4868495 (17.89%) aligned concordantly >1 times 32.47% overall alignment rate 27212918 reads; of these: 27212918 (100.00%) were paired; of these: 18517573 (68.05%) aligned concordantly 0 times 3909659 (14.37%) aligned concordantly exactly 1 time 4785686 (17.59%) aligned concordantly >1 times 31.95% overall alignment rate Processed 27212918 sequences in total Successfully deleted the temporary files EPI-181_S16_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-181_S16_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27212918 Number of paired-end alignments with a unique best hit: 10790981 Mapping efficiency: 39.7% Sequence pairs with no alignments under any condition: 14282015 Sequence pairs did not map uniquely: 2139922 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: 5313318 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5477662 ((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: 336107175 Total methylated C's in CpG context: 13211112 Total methylated C's in CHG context: 1652081 Total methylated C's in CHH context: 3893943 Total methylated C's in Unknown context: 60101 Total unmethylated C's in CpG context: 34596724 Total unmethylated C's in CHG context: 71273976 Total unmethylated C's in CHH context: 211479339 Total unmethylated C's in Unknown context: 733272 C methylated in CpG context: 27.6% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 7.6% Bismark completed in 0d 1h 41m 51s ==================== 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_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/sr320/0807-003 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-182_S17_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-182_S17_L003_R1_001_val_1.fq.gz to EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-182_S17_L003_R1_001_val_1.fq.gz (31499315 sequences in total) Writing a G -> A converted version of the input file EPI-182_S17_L003_R2_001_val_2.fq.gz to EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-182_S17_L003_R2_001_val_2.fq.gz (31499315 sequences in total) Input files are EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_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-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_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:3:1107:2786:2250_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TGATTNTATTATGGAAATATTGTTTAGTTTAGTAGAAATATTTTTTGGAGTTGTTGTGA BBBBB#<>> Writing bisulfite mapping results to EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_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 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far 31499315 reads; of these: 31499315 (100.00%) were paired; of these: 20639641 (65.52%) aligned concordantly 0 times 4805807 (15.26%) aligned concordantly exactly 1 time 6053867 (19.22%) aligned concordantly >1 times 34.48% overall alignment rate 31499315 reads; of these: 31499315 (100.00%) were paired; of these: 20717975 (65.77%) aligned concordantly 0 times 4809206 (15.27%) aligned concordantly exactly 1 time 5972134 (18.96%) aligned concordantly >1 times 34.23% overall alignment rate Processed 31499315 sequences in total Successfully deleted the temporary files EPI-182_S17_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-182_S17_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 31499315 Number of paired-end alignments with a unique best hit: 13143700 Mapping efficiency: 41.7% Sequence pairs with no alignments under any condition: 15672601 Sequence pairs did not map uniquely: 2683014 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: 6520043 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6623657 ((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: 407184402 Total methylated C's in CpG context: 14617019 Total methylated C's in CHG context: 1959865 Total methylated C's in CHH context: 4544903 Total methylated C's in Unknown context: 72663 Total unmethylated C's in CpG context: 40997905 Total unmethylated C's in CHG context: 84917152 Total unmethylated C's in CHH context: 260147558 Total unmethylated C's in Unknown context: 900486 C methylated in CpG context: 26.3% C methylated in CHG context: 2.3% C methylated in CHH context: 1.7% C methylated in unknown context (CN or CHN): 7.5% Bismark completed in 0d 2h 4m 3s ==================== 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_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/sr320/0807-003 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-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-184_S18_L003_R1_001_val_1.fq.gz to EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-184_S18_L003_R1_001_val_1.fq.gz (20689148 sequences in total) Writing a G -> A converted version of the input file EPI-184_S18_L003_R2_001_val_2.fq.gz to EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-184_S18_L003_R2_001_val_2.fq.gz (20689148 sequences in total) Input files are EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_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-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_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:3:1107:2159:2247_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 GAATANGGAAATGGGTAGGATGTAGGTTATAAAGGAAATTGGGTTAATAATGTGAATAGAGAAATGGGTAGGAGGTAGGTTATAAAGGAAATTGGGT BBBBB#B>> Writing bisulfite mapping results to EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2211:18307:25265_1:N:0:ACAGTG PGA_scaffold9__45_contigs__length_38581958 2 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2204:5160:88396_1:N:0:ACAGTG PGA_scaffold8__63_contigs__length_61151155 61151067 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 20689148 reads; of these: 20689148 (100.00%) were paired; of these: 13581727 (65.65%) aligned concordantly 0 times 3064795 (14.81%) aligned concordantly exactly 1 time 4042626 (19.54%) aligned concordantly >1 times 34.35% overall alignment rate 20689148 reads; of these: 20689148 (100.00%) were paired; of these: 13516815 (65.33%) aligned concordantly 0 times 3053788 (14.76%) aligned concordantly exactly 1 time 4118545 (19.91%) aligned concordantly >1 times 34.67% overall alignment rate Processed 20689148 sequences in total Successfully deleted the temporary files EPI-184_S18_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-184_S18_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 20689148 Number of paired-end alignments with a unique best hit: 8444730 Mapping efficiency: 40.8% Sequence pairs with no alignments under any condition: 10305796 Sequence pairs did not map uniquely: 1938622 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: 4167553 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4277175 ((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: 251839676 Total methylated C's in CpG context: 9669457 Total methylated C's in CHG context: 1217679 Total methylated C's in CHH context: 3983200 Total methylated C's in Unknown context: 60694 Total unmethylated C's in CpG context: 25706227 Total unmethylated C's in CHG context: 53487968 Total unmethylated C's in CHH context: 157775145 Total unmethylated C's in Unknown context: 557312 C methylated in CpG context: 27.3% C methylated in CHG context: 2.2% C methylated in CHH context: 2.5% C methylated in unknown context (CN or CHN): 9.8% Bismark completed in 0d 1h 21m 40s ==================== 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_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/sr320/0807-003 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-185_S19_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-185_S19_L003_R1_001_val_1.fq.gz to EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-185_S19_L003_R1_001_val_1.fq.gz (11003725 sequences in total) Writing a G -> A converted version of the input file EPI-185_S19_L003_R2_001_val_2.fq.gz to EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-185_S19_L003_R2_001_val_2.fq.gz (11003725 sequences in total) Input files are EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_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-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_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:3:1107:4218:2247_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 GGGGANGGAGAGTTATAGGTAGTTGTAGTGGATATGTTGTGGGATTGAGGATGTTGTGTTGTGTTTTATGGTTTTGGGTTGTTGTTGTAGAGTTGAATTTG BBBBB#B>> Writing bisulfite mapping results to EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_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 11003725 reads; of these: 11003725 (100.00%) were paired; of these: 7568004 (68.78%) aligned concordantly 0 times 1482121 (13.47%) aligned concordantly exactly 1 time 1953600 (17.75%) aligned concordantly >1 times 31.22% overall alignment rate 11003725 reads; of these: 11003725 (100.00%) were paired; of these: 7619058 (69.24%) aligned concordantly 0 times 1471639 (13.37%) aligned concordantly exactly 1 time 1913028 (17.39%) aligned concordantly >1 times 30.76% overall alignment rate Processed 11003725 sequences in total Successfully deleted the temporary files EPI-185_S19_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-185_S19_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 11003725 Number of paired-end alignments with a unique best hit: 4103253 Mapping efficiency: 37.3% Sequence pairs with no alignments under any condition: 6008199 Sequence pairs did not map uniquely: 892273 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: 2013443 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2089810 ((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: 125649607 Total methylated C's in CpG context: 4647874 Total methylated C's in CHG context: 682027 Total methylated C's in CHH context: 3288445 Total methylated C's in Unknown context: 50440 Total unmethylated C's in CpG context: 13300931 Total unmethylated C's in CHG context: 26446504 Total unmethylated C's in CHH context: 77283826 Total unmethylated C's in Unknown context: 276168 C methylated in CpG context: 25.9% C methylated in CHG context: 2.5% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 15.4% Bismark completed in 0d 0h 39m 15s ==================== 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_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/sr320/0807-003 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-187_S20_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-187_S20_L003_R1_001_val_1.fq.gz to EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-187_S20_L003_R1_001_val_1.fq.gz (22734395 sequences in total) Writing a G -> A converted version of the input file EPI-187_S20_L003_R2_001_val_2.fq.gz to EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-187_S20_L003_R2_001_val_2.fq.gz (22734395 sequences in total) Input files are EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_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-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_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:3:1107:5270:2246_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TAATANATAATTATTTTAGATAATAAGGTTGGAAAAATTGTTGAAATATGGGTTTATTTTTTGTTTTATTGTTTGTAAATTTAGTGTTGAGTTATTGT BBBBB#BBBFFFFFFFFBFFFFFFBBFFF>> Writing bisulfite mapping results to EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2312:4165:2931_1:N:0:CAGATC PGA_scaffold9__45_contigs__length_38581958 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2204:7022:13811_1:N:0:CAGATC PGA_scaffold16__33_contigs__length_31980953 1 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2112:6280:50513_1:N:0:CAGATC PGA_scaffold16__33_contigs__length_31980953 2 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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1111:19003:88210_1:N:0:CAGATC PGA_scaffold16__33_contigs__length_31980953 2 Processed 22000000 sequence pairs so far 22734395 reads; of these: 22734395 (100.00%) were paired; of these: 14659250 (64.48%) aligned concordantly 0 times 3540890 (15.58%) aligned concordantly exactly 1 time 4534255 (19.94%) aligned concordantly >1 times 35.52% overall alignment rate 22734395 reads; of these: 22734395 (100.00%) were paired; of these: 14778776 (65.01%) aligned concordantly 0 times 3507484 (15.43%) aligned concordantly exactly 1 time 4448135 (19.57%) aligned concordantly >1 times 34.99% overall alignment rate Processed 22734395 sequences in total Successfully deleted the temporary files EPI-187_S20_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-187_S20_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22734395 Number of paired-end alignments with a unique best hit: 9655534 Mapping efficiency: 42.5% Sequence pairs with no alignments under any condition: 10981695 Sequence pairs did not map uniquely: 2097166 Sequence pairs which were discarded because genomic sequence could not be extracted: 4 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4757885 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4897645 ((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: 292287685 Total methylated C's in CpG context: 12549941 Total methylated C's in CHG context: 1572027 Total methylated C's in CHH context: 3841851 Total methylated C's in Unknown context: 60882 Total unmethylated C's in CpG context: 29075423 Total unmethylated C's in CHG context: 62324170 Total unmethylated C's in CHH context: 182924273 Total unmethylated C's in Unknown context: 633983 C methylated in CpG context: 30.1% C methylated in CHG context: 2.5% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 8.8% Bismark completed in 0d 1h 29m 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_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/sr320/0807-003 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-188_S21_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-188_S21_L003_R1_001_val_1.fq.gz to EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-188_S21_L003_R1_001_val_1.fq.gz (21488138 sequences in total) Writing a G -> A converted version of the input file EPI-188_S21_L003_R2_001_val_2.fq.gz to EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-188_S21_L003_R2_001_val_2.fq.gz (21488138 sequences in total) Input files are EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_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-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_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:3:1107:6853:2249_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AGTTGNGGGTAAGAGAGAGTTTTTTTGGAAAATTTTGATATTTTAAAAGTTAAATAATGTATTATAGTAAGTTTTATAGTGTATGAGGGG BBBBB#>> Writing bisulfite mapping results to EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_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 D00743:144:CAAWNANXX:3:2205:11759:30686_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 1 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 21488138 reads; of these: 21488138 (100.00%) were paired; of these: 14059030 (65.43%) aligned concordantly 0 times 3145929 (14.64%) aligned concordantly exactly 1 time 4283179 (19.93%) aligned concordantly >1 times 34.57% overall alignment rate 21488138 reads; of these: 21488138 (100.00%) were paired; of these: 13990818 (65.11%) aligned concordantly 0 times 3141180 (14.62%) aligned concordantly exactly 1 time 4356140 (20.27%) aligned concordantly >1 times 34.89% overall alignment rate Processed 21488138 sequences in total Successfully deleted the temporary files EPI-188_S21_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-188_S21_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 21488138 Number of paired-end alignments with a unique best hit: 8423411 Mapping efficiency: 39.2% Sequence pairs with no alignments under any condition: 10776872 Sequence pairs did not map uniquely: 2287855 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: 4160590 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4262820 ((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: 235029500 Total methylated C's in CpG context: 8853859 Total methylated C's in CHG context: 1292583 Total methylated C's in CHH context: 3088082 Total methylated C's in Unknown context: 52541 Total unmethylated C's in CpG context: 25257864 Total unmethylated C's in CHG context: 49422337 Total unmethylated C's in CHH context: 147114775 Total unmethylated C's in Unknown context: 499727 C methylated in CpG context: 26.0% C methylated in CHG context: 2.5% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 9.5% Bismark completed in 0d 1h 17m 38s ==================== 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_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/sr320/0807-003 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-193_S22_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-193_S22_L003_R1_001_val_1.fq.gz to EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-193_S22_L003_R1_001_val_1.fq.gz (26770469 sequences in total) Writing a G -> A converted version of the input file EPI-193_S22_L003_R2_001_val_2.fq.gz to EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-193_S22_L003_R2_001_val_2.fq.gz (26770469 sequences in total) Input files are EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_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-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_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:3:1107:3001:2249_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 ATTGTNTATAATTTTGGTATAGTTTTATGTAGTTGGGGATATTTAGGGATATTGTATATAATTTTGGTATAGTTTTGTAAAGTTAGGGATATTTAGGG /B/BB#//>> Writing bisulfite mapping results to EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_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 26770469 reads; of these:26770469 reads; of these: 26770469 (26770469 (100.00100.00%%) were paired; of these:) were paired; of these: 1740182617323811 ( (65.0064.71%%) aligned concordantly 0 times) aligned concordantly 0 times 39834283958282 ( (14.8814.79%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 53852155488376 ( (20.1220.50%%) aligned concordantly >1 times) aligned concordantly >1 times 35.0035.29%% overall alignment rate overall alignment rate Processed 26770469 sequences in total Successfully deleted the temporary files EPI-193_S22_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-193_S22_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 26770469 Number of paired-end alignments with a unique best hit: 10697352 Mapping efficiency: 40.0% Sequence pairs with no alignments under any condition: 13242455 Sequence pairs did not map uniquely: 2830662 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: 5278754 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5418598 ((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: 301211333 Total methylated C's in CpG context: 12254387 Total methylated C's in CHG context: 1506836 Total methylated C's in CHH context: 3959201 Total methylated C's in Unknown context: 62246 Total unmethylated C's in CpG context: 30734018 Total unmethylated C's in CHG context: 63666955 Total unmethylated C's in CHH context: 189089936 Total unmethylated C's in Unknown context: 644527 C methylated in CpG context: 28.5% C methylated in CHG context: 2.3% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 8.8% Bismark completed in 0d 1h 38m 44s ==================== 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_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/sr320/0807-003 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-194_S23_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-194_S23_L003_R1_001_val_1.fq.gz to EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-194_S23_L003_R1_001_val_1.fq.gz (27459153 sequences in total) Writing a G -> A converted version of the input file EPI-194_S23_L003_R2_001_val_2.fq.gz to EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-194_S23_L003_R2_001_val_2.fq.gz (27459153 sequences in total) Input files are EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_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-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_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:3:1107:4438:2247_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 TTAGTNATTAAGGGGTTGTGTGTTTGAATTTTTTGTTTGGTAATAGTTTTTGTGATGATTGATATATGATATTGTGTTTTATTATTATTTGTTTTTTA BBBBB#BBB>> Writing bisulfite mapping results to EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_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 27459153 reads; of these: 27459153 (100.00%) were paired; of these: 18108485 (65.95%) aligned concordantly 0 times 4245947 (15.46%) aligned concordantly exactly 1 time 5104721 (18.59%) aligned concordantly >1 times 34.05% overall alignment rate 27459153 reads; of these: 27459153 (100.00%) were paired; of these: 17993725 (65.53%) aligned concordantly 0 times 4268412 (15.54%) aligned concordantly exactly 1 time 5197016 (18.93%) aligned concordantly >1 times 34.47% overall alignment rate Processed 27459153 sequences in total Successfully deleted the temporary files EPI-194_S23_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-194_S23_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27459153 Number of paired-end alignments with a unique best hit: 11624042 Mapping efficiency: 42.3% Sequence pairs with no alignments under any condition: 13557404 Sequence pairs did not map uniquely: 2277707 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: 5726606 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5897436 ((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: 360459395 Total methylated C's in CpG context: 15208121 Total methylated C's in CHG context: 1730704 Total methylated C's in CHH context: 4696700 Total methylated C's in Unknown context: 66894 Total unmethylated C's in CpG context: 35095565 Total unmethylated C's in CHG context: 75921624 Total unmethylated C's in CHH context: 227806681 Total unmethylated C's in Unknown context: 771714 C methylated in CpG context: 30.2% C methylated in CHG context: 2.2% C methylated in CHH context: 2.0% C methylated in unknown context (CN or CHN): 8.0% Bismark completed in 0d 1h 51m 59s ==================== 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_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/sr320/0807-003 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-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-199_S24_L003_R1_001_val_1.fq.gz to EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-199_S24_L003_R1_001_val_1.fq.gz (15913069 sequences in total) Writing a G -> A converted version of the input file EPI-199_S24_L003_R2_001_val_2.fq.gz to EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-199_S24_L003_R2_001_val_2.fq.gz (15913069 sequences in total) Input files are EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_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-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_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:3:1107:3720:2249_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 ATTAGNTTTTTATATTTAAGGAGATTGAGAGATATATTGTGAATTTTGAAAGAAAATTGAAAGAGGTTATTGAAGAAAGAGGTATGTG BBBBB#BB>> Writing bisulfite mapping results to EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_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 15913069 reads; of these: 15913069 (100.00%) were paired; of these: 10515513 (66.08%) aligned concordantly 0 times 2317383 (14.56%) aligned concordantly exactly 1 time 3080173 (19.36%) aligned concordantly >1 times 33.92% overall alignment rate 15913069 reads; of these: 15913069 (100.00%) were paired; of these: 10578681 (66.48%) aligned concordantly 0 times 2317757 (14.57%) aligned concordantly exactly 1 time 3016631 (18.96%) aligned concordantly >1 times 33.52% overall alignment rate Processed 15913069 sequences in total Successfully deleted the temporary files EPI-199_S24_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-199_S24_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 15913069 Number of paired-end alignments with a unique best hit: 6267321 Mapping efficiency: 39.4% Sequence pairs with no alignments under any condition: 8113691 Sequence pairs did not map uniquely: 1532057 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: 3085988 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3181333 ((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: 181304638 Total methylated C's in CpG context: 8091308 Total methylated C's in CHG context: 993527 Total methylated C's in CHH context: 3522698 Total methylated C's in Unknown context: 63898 Total unmethylated C's in CpG context: 17646077 Total unmethylated C's in CHG context: 38210008 Total unmethylated C's in CHH context: 112841020 Total unmethylated C's in Unknown context: 386634 C methylated in CpG context: 31.4% C methylated in CHG context: 2.5% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 14.2% Bismark completed in 0d 1h 0m 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/sr320/0807-003'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_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/sr320/0807-003 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-200_S25_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-200_S25_L003_R1_001_val_1.fq.gz to EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-200_S25_L003_R1_001_val_1.fq.gz (25100695 sequences in total) Writing a G -> A converted version of the input file EPI-200_S25_L003_R2_001_val_2.fq.gz to EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-200_S25_L003_R2_001_val_2.fq.gz (25100695 sequences in total) Input files are EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_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-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_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:3:1107:4688:2247_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 GTATGNTGTTTATGTGTTTTAGAGGTGGAGTATTGGATTAATGATAA BBBBB#BBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:3:1107:4688:2247_2:N:0:CTTGTA/2 141 * 0 0 * * 0 0 TTANCANNNNNNNNNNNNNNNNNCTNTNNNNNACATAAACACCATAC BBB#BB#################B<#B#####BBBFFFFFFFFFFFF YT:Z:UP YF:Z:NS Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_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 --nofw)) Found first alignment: D00743:144:CAAWNANXX:3:1107:4688:2247_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 GTATGNTGTTTATGTGTTTTAGAGGTGGAGTATTGGATTAATGATAA BBBBB#BBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:3:1107:4688:2247_2:N:0:CTTGTA/2 141 * 0 0 * * 0 0 TTANCANNNNNNNNNNNNNNNNNCTNTNNNNNACATAAACACCATAC BBB#BB#################B<#B#####BBBFFFFFFFFFFFF YT:Z:UP YF:Z:NS >>> Writing bisulfite mapping results to EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_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:3:2101:4656:49942_1:N:0:CTTGTA PGA_scaffold9__45_contigs__length_38581958 2 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 25100695 reads; of these: 25100695 (100.00%) were paired; of these: 16002055 (63.75%) aligned concordantly 0 times 3838624 (15.29%) aligned concordantly exactly 1 time 5260016 (20.96%) aligned concordantly >1 times 36.25% overall alignment rate 25100695 reads; of these: 25100695 (100.00%) were paired; of these: 15917679 (63.42%) aligned concordantly 0 times 3833844 (15.27%) aligned concordantly exactly 1 time 5349172 (21.31%) aligned concordantly >1 times 36.58% overall alignment rate Processed 25100695 sequences in total Successfully deleted the temporary files EPI-200_S25_L003_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-200_S25_L003_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 25100695 Number of paired-end alignments with a unique best hit: 10396122 Mapping efficiency: 41.4% Sequence pairs with no alignments under any condition: 11933311 Sequence pairs did not map uniquely: 2771262 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: 5128955 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5267166 ((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: 292335065 Total methylated C's in CpG context: 12585999 Total methylated C's in CHG context: 1652750 Total methylated C's in CHH context: 4231978 Total methylated C's in Unknown context: 79283 Total unmethylated C's in CpG context: 28671686 Total unmethylated C's in CHG context: 61623093 Total unmethylated C's in CHH context: 183569559 Total unmethylated C's in Unknown context: 639910 C methylated in CpG context: 30.5% C methylated in CHG context: 2.6% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 11.0% Bismark completed in 0d 1h 36m 28s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): EPI-175_S14_L003_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-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam: 10209529 Total number duplicated alignments removed: 2284909 (22.38%) Duplicated alignments were found at: 1428268 different position(s) Total count of deduplicated leftover sequences: 7924620 (77.62% 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-175_S14_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-176_S15_L003_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-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam: 13724717 Total number duplicated alignments removed: 3630031 (26.45%) Duplicated alignments were found at: 2189122 different position(s) Total count of deduplicated leftover sequences: 10094686 (73.55% 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-176_S15_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-181_S16_L003_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-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam: 10790980 Total number duplicated alignments removed: 2580715 (23.92%) Duplicated alignments were found at: 1499838 different position(s) Total count of deduplicated leftover sequences: 8210265 (76.08% 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-181_S16_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-182_S17_L003_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-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam: 13143700 Total number duplicated alignments removed: 2877178 (21.89%) Duplicated alignments were found at: 1635843 different position(s) Total count of deduplicated leftover sequences: 10266522 (78.11% 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-182_S17_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-184_S18_L003_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-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam: 8444728 Total number duplicated alignments removed: 2148266 (25.44%) Duplicated alignments were found at: 1332291 different position(s) Total count of deduplicated leftover sequences: 6296462 (74.56% 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-184_S18_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-185_S19_L003_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-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam: 4103253 Total number duplicated alignments removed: 1336980 (32.58%) Duplicated alignments were found at: 804018 different position(s) Total count of deduplicated leftover sequences: 2766273 (67.42% 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-185_S19_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-187_S20_L003_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-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam: 9655530 Total number duplicated alignments removed: 2556625 (26.48%) Duplicated alignments were found at: 1509525 different position(s) Total count of deduplicated leftover sequences: 7098905 (73.52% 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-187_S20_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-188_S21_L003_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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam: 8423410 Total number duplicated alignments removed: 2230577 (26.48%) Duplicated alignments were found at: 1361870 different position(s) Total count of deduplicated leftover sequences: 6192833 (73.52% 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-188_S21_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-193_S22_L003_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-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam: 10697352 Total number duplicated alignments removed: 2526429 (23.62%) Duplicated alignments were found at: 1585629 different position(s) Total count of deduplicated leftover sequences: 8170923 (76.38% 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-193_S22_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-194_S23_L003_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-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam: 11624042 Total number duplicated alignments removed: 2623096 (22.57%) Duplicated alignments were found at: 1648237 different position(s) Total count of deduplicated leftover sequences: 9000946 (77.43% 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-194_S23_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-199_S24_L003_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-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam: 6267321 Total number duplicated alignments removed: 1900244 (30.32%) Duplicated alignments were found at: 1204077 different position(s) Total count of deduplicated leftover sequences: 4367077 (69.68% 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-199_S24_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-200_S25_L003_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-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam: 10396121 Total number duplicated alignments removed: 2895134 (27.85%) Duplicated alignments were found at: 1778247 different position(s) Total count of deduplicated leftover sequences: 7500987 (72.15% 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-200_S25_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_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-175_S14_L003_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/sr320/0807-003') 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-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-175_S14_L003_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-175_S14_L003_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-175_S14_L003_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-175_S14_L003_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-175_S14_L003_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-175_S14_L003_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-175_S14_L003_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-175_S14_L003_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-175_S14_L003_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-175_S14_L003_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-175_S14_L003_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-175_S14_L003_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-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_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-175_S14_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_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 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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.. 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.. Merging individual splitting reports into overall report: 'EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7924620 lines in total Total number of methylation call strings processed: 15849240 Final Cytosine Methylation Report ================================= Total number of C's analysed: 169230320 Total methylated C's in CpG context: 6854838 Total methylated C's in CHG context: 805593 Total methylated C's in CHH context: 2153742 Total C to T conversions in CpG context: 16729782 Total C to T conversions in CHG context: 34594121 Total C to T conversions in CHH context: 108092244 C methylated in CpG context: 29.1% C methylated in CHG context: 2.3% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-175_S14_L003_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-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-175_S14_L003_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/sr320/0807-003/CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-175_S14_L003_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-175_S14_L003_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-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-175_S14_L003_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-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-176_S15_L003_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-176_S15_L003_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-176_S15_L003_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-176_S15_L003_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-176_S15_L003_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-176_S15_L003_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-176_S15_L003_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-176_S15_L003_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-176_S15_L003_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-176_S15_L003_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-176_S15_L003_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-176_S15_L003_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-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-176_S15_L003_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-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-176_S15_L003_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-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-176_S15_L003_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-176_S15_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-176_S15_L003_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.. Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 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.. Processed lines: 10000000 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.. Processed lines: 10000000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10094686 lines in total Total number of methylation call strings processed: 20189372 Final Cytosine Methylation Report ================================= Total number of C's analysed: 212732771 Total methylated C's in CpG context: 8409431 Total methylated C's in CHG context: 937010 Total methylated C's in CHH context: 2366691 Total C to T conversions in CpG context: 21389527 Total C to T conversions in CHG context: 42655847 Total C to T conversions in CHH context: 136974265 C methylated in CpG context: 28.2% C methylated in CHG context: 2.1% C methylated in CHH context: 1.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-176_S15_L003_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-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-176_S15_L003_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/sr320/0807-003/CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-176_S15_L003_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-176_S15_L003_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-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-176_S15_L003_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-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-181_S16_L003_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-181_S16_L003_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-181_S16_L003_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-181_S16_L003_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-181_S16_L003_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-181_S16_L003_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-181_S16_L003_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-181_S16_L003_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-181_S16_L003_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-181_S16_L003_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-181_S16_L003_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-181_S16_L003_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-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-181_S16_L003_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-181_S16_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_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: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 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.. 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.. Processed lines: 8000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8210265 lines in total Total number of methylation call strings processed: 16420530 Final Cytosine Methylation Report ================================= Total number of C's analysed: 182131746 Total methylated C's in CpG context: 7773669 Total methylated C's in CHG context: 910797 Total methylated C's in CHH context: 2287864 Total C to T conversions in CpG context: 17313389 Total C to T conversions in CHG context: 37265101 Total C to T conversions in CHH context: 116580926 C methylated in CpG context: 31.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-181_S16_L003_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-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-181_S16_L003_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/sr320/0807-003/CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-181_S16_L003_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-181_S16_L003_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-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-181_S16_L003_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-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-182_S17_L003_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-182_S17_L003_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-182_S17_L003_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-182_S17_L003_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-182_S17_L003_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-182_S17_L003_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-182_S17_L003_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-182_S17_L003_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-182_S17_L003_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-182_S17_L003_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-182_S17_L003_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-182_S17_L003_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-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-182_S17_L003_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-182_S17_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-182_S17_L003_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: 9500000 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 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.. 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-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10266522 lines in total Total number of methylation call strings processed: 20533044 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222524486 Total methylated C's in CpG context: 8754862 Total methylated C's in CHG context: 1102130 Total methylated C's in CHH context: 2694418 Total C to T conversions in CpG context: 21458168 Total C to T conversions in CHG context: 44943458 Total C to T conversions in CHH context: 143571450 C methylated in CpG context: 29.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-182_S17_L003_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-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-182_S17_L003_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/sr320/0807-003/CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-182_S17_L003_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-182_S17_L003_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-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-182_S17_L003_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-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-184_S18_L003_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-184_S18_L003_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-184_S18_L003_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-184_S18_L003_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-184_S18_L003_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-184_S18_L003_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-184_S18_L003_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-184_S18_L003_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-184_S18_L003_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-184_S18_L003_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-184_S18_L003_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-184_S18_L003_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-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-184_S18_L003_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-184_S18_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_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-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6296462 lines in total Total number of methylation call strings processed: 12592924 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128398540 Total methylated C's in CpG context: 5213255 Total methylated C's in CHG context: 627120 Total methylated C's in CHH context: 2204316 Total C to T conversions in CpG context: 12567730 Total C to T conversions in CHG context: 26364706 Total C to T conversions in CHH context: 81421413 C methylated in CpG context: 29.3% C methylated in CHG context: 2.3% C methylated in CHH context: 2.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-184_S18_L003_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-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-184_S18_L003_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/sr320/0807-003/CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-184_S18_L003_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-184_S18_L003_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-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-184_S18_L003_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-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-185_S19_L003_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-185_S19_L003_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-185_S19_L003_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-185_S19_L003_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-185_S19_L003_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-185_S19_L003_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-185_S19_L003_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-185_S19_L003_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-185_S19_L003_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-185_S19_L003_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-185_S19_L003_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-185_S19_L003_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-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-185_S19_L003_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-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-185_S19_L003_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-185_S19_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-185_S19_L003_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 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.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 2766273 lines in total Total number of methylation call strings processed: 5532546 Final Cytosine Methylation Report ================================= Total number of C's analysed: 57532394 Total methylated C's in CpG context: 2287343 Total methylated C's in CHG context: 323890 Total methylated C's in CHH context: 1768982 Total C to T conversions in CpG context: 5639671 Total C to T conversions in CHG context: 11658279 Total C to T conversions in CHH context: 35854229 C methylated in CpG context: 28.9% C methylated in CHG context: 2.7% C methylated in CHH context: 4.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-185_S19_L003_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-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-185_S19_L003_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/sr320/0807-003/CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-185_S19_L003_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-185_S19_L003_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-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-185_S19_L003_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-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-187_S20_L003_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-187_S20_L003_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-187_S20_L003_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-187_S20_L003_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-187_S20_L003_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-187_S20_L003_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-187_S20_L003_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-187_S20_L003_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-187_S20_L003_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-187_S20_L003_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-187_S20_L003_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-187_S20_L003_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-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-187_S20_L003_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-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-187_S20_L003_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-187_S20_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_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 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 7000000 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: 7000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 7000000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7098905 lines in total Total number of methylation call strings processed: 14197810 Final Cytosine Methylation Report ================================= Total number of C's analysed: 150742463 Total methylated C's in CpG context: 6936899 Total methylated C's in CHG context: 814250 Total methylated C's in CHH context: 2156222 Total C to T conversions in CpG context: 13822954 Total C to T conversions in CHG context: 31050905 Total C to T conversions in CHH context: 95961233 C methylated in CpG context: 33.4% C methylated in CHG context: 2.6% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-187_S20_L003_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-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-187_S20_L003_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/sr320/0807-003/CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-187_S20_L003_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-187_S20_L003_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-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-187_S20_L003_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-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-188_S21_L003_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-188_S21_L003_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-188_S21_L003_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-188_S21_L003_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-188_S21_L003_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-188_S21_L003_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-188_S21_L003_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-188_S21_L003_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-188_S21_L003_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-188_S21_L003_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-188_S21_L003_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-188_S21_L003_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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-188_S21_L003_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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-188_S21_L003_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-188_S21_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_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: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 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 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.. Processed lines: 6000000 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.. Processed lines: 6000000 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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6192833 lines in total Total number of methylation call strings processed: 12385666 Final Cytosine Methylation Report ================================= Total number of C's analysed: 115906900 Total methylated C's in CpG context: 4644294 Total methylated C's in CHG context: 619856 Total methylated C's in CHH context: 1638581 Total C to T conversions in CpG context: 11620008 Total C to T conversions in CHG context: 23551619 Total C to T conversions in CHH context: 73832542 C methylated in CpG context: 28.6% C methylated in CHG context: 2.6% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-188_S21_L003_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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-188_S21_L003_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/sr320/0807-003/CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-188_S21_L003_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-188_S21_L003_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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-188_S21_L003_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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-193_S22_L003_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-193_S22_L003_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-193_S22_L003_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-193_S22_L003_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-193_S22_L003_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-193_S22_L003_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-193_S22_L003_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-193_S22_L003_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-193_S22_L003_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-193_S22_L003_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-193_S22_L003_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-193_S22_L003_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-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-193_S22_L003_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-193_S22_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_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: 7500000 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 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.. 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-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8170923 lines in total Total number of methylation call strings processed: 16341846 Final Cytosine Methylation Report ================================= Total number of C's analysed: 156322050 Total methylated C's in CpG context: 6612365 Total methylated C's in CHG context: 770831 Total methylated C's in CHH context: 2168983 Total C to T conversions in CpG context: 15198462 Total C to T conversions in CHG context: 31981857 Total C to T conversions in CHH context: 99589552 C methylated in CpG context: 30.3% C methylated in CHG context: 2.4% C methylated in CHH context: 2.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-193_S22_L003_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-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-193_S22_L003_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/sr320/0807-003/CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-193_S22_L003_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-193_S22_L003_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-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-193_S22_L003_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-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-194_S23_L003_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-194_S23_L003_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-194_S23_L003_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-194_S23_L003_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-194_S23_L003_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-194_S23_L003_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-194_S23_L003_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-194_S23_L003_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-194_S23_L003_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-194_S23_L003_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-194_S23_L003_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-194_S23_L003_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-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-194_S23_L003_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-194_S23_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_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 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Finished processing child process. Exiting.. Processed lines: 9000000 Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9000946 lines in total Total number of methylation call strings processed: 18001892 Final Cytosine Methylation Report ================================= Total number of C's analysed: 203726589 Total methylated C's in CpG context: 8959141 Total methylated C's in CHG context: 996952 Total methylated C's in CHH context: 2787951 Total C to T conversions in CpG context: 18995825 Total C to T conversions in CHG context: 41660215 Total C to T conversions in CHH context: 130326505 C methylated in CpG context: 32.0% C methylated in CHG context: 2.3% C methylated in CHH context: 2.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-194_S23_L003_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-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-194_S23_L003_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/sr320/0807-003/CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-194_S23_L003_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-194_S23_L003_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-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-194_S23_L003_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-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-199_S24_L003_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-199_S24_L003_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-199_S24_L003_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-199_S24_L003_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-199_S24_L003_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-199_S24_L003_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-199_S24_L003_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-199_S24_L003_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-199_S24_L003_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-199_S24_L003_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-199_S24_L003_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-199_S24_L003_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-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-199_S24_L003_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-199_S24_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_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 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4367077 lines in total Total number of methylation call strings processed: 8734154 Final Cytosine Methylation Report ================================= Total number of C's analysed: 88024093 Total methylated C's in CpG context: 4047323 Total methylated C's in CHG context: 479419 Total methylated C's in CHH context: 1871691 Total C to T conversions in CpG context: 8070663 Total C to T conversions in CHG context: 17975035 Total C to T conversions in CHH context: 55579962 C methylated in CpG context: 33.4% C methylated in CHG context: 2.6% C methylated in CHH context: 3.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-199_S24_L003_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-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-199_S24_L003_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/sr320/0807-003/CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-199_S24_L003_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-199_S24_L003_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-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-199_S24_L003_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-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-200_S25_L003_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-200_S25_L003_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-200_S25_L003_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-200_S25_L003_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-200_S25_L003_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-200_S25_L003_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-200_S25_L003_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-200_S25_L003_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-200_S25_L003_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-200_S25_L003_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-200_S25_L003_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-200_S25_L003_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-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-200_S25_L003_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-200_S25_L003_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_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 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Processed lines: 7500000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7500987 lines in total Total number of methylation call strings processed: 15001974 Final Cytosine Methylation Report ================================= Total number of C's analysed: 143389134 Total methylated C's in CpG context: 6473128 Total methylated C's in CHG context: 794893 Total methylated C's in CHH context: 2249885 Total C to T conversions in CpG context: 13251440 Total C to T conversions in CHG context: 29375321 Total C to T conversions in CHH context: 91244467 C methylated in CpG context: 32.8% C methylated in CHG context: 2.6% C methylated in CHH context: 2.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-200_S25_L003_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-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-200_S25_L003_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/sr320/0807-003/CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/0807-003/CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-200_S25_L003_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-200_S25_L003_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-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-200_S25_L003_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-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 12 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-175_S14_L003_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-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-176_S15_L003_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-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-181_S16_L003_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-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-182_S17_L003_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-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-184_S18_L003_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-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-185_S19_L003_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-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-187_S20_L003_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-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-188_S21_L003_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-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-193_S22_L003_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-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-194_S23_L003_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-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-199_S24_L003_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-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-200_S25_L003_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 12 Bismark BAM file(s)... >> Reading from Bismark report: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-200_S25_L003_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...