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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-103_S27_L005_R1_001_val_1.fq.gz to EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-103_S27_L005_R1_001_val_1.fq.gz (20349659 sequences in total) Writing a G -> A converted version of the input file EPI-103_S27_L005_R2_001_val_2.fq.gz to EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-103_S27_L005_R2_001_val_2.fq.gz (20349659 sequences in total) Input files are EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1512:1956_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 NGTTTATATGTATGTATTATATTTGTGTAGGTATTGTATTTGATAAGGAT #<<>> Writing bisulfite mapping results to EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2303:16672:27349_1:N:0:ATCACG Scaffold_09 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far 20349659 reads; of these: 20349659 (100.00%) were paired; of these: 13027775 (64.02%) aligned concordantly 0 times 3373694 (16.58%) aligned concordantly exactly 1 time 3948190 (19.4020349659% reads; of these:) aligned concordantly >1 times 35.98 %20349659 overall alignment rate ( 100.00%) were paired; of these: 13093446 (64.34%) aligned concordantly 0 times 3361315 (16.52%) aligned concordantly exactly 1 time 3894898 (19.14%) aligned concordantly >1 times 35.66% overall alignment rate Processed 20349659 sequences in total Successfully deleted the temporary files EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-103_S27_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 20349659 Number of paired-end alignments with a unique best hit: 9095592 Mapping efficiency: 44.7% Sequence pairs with no alignments under any condition: 9572011 Sequence pairs did not map uniquely: 1682056 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4509438 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4586153 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 289949317 Total methylated C's in CpG context: 9619421 Total methylated C's in CHG context: 1310642 Total methylated C's in CHH context: 2350411 Total methylated C's in Unknown context: 40612 Total unmethylated C's in CpG context: 31065297 Total unmethylated C's in CHG context: 59905410 Total unmethylated C's in CHH context: 185698136 Total unmethylated C's in Unknown context: 609374 C methylated in CpG context: 23.6% C methylated in CHG context: 2.1% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.2% Bismark completed in 0d 1h 14m 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-104_S28_L005_R1_001_val_1.fq.gz to EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-104_S28_L005_R1_001_val_1.fq.gz (30015261 sequences in total) Writing a G -> A converted version of the input file EPI-104_S28_L005_R2_001_val_2.fq.gz to EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-104_S28_L005_R2_001_val_2.fq.gz (30015261 sequences in total) Input files are EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1112:1988_1:N:0:CGATGT/1 99 Scaffold_05_CT_converted 17340906 1 101M = 17341304 497 NGGTGGTAGTTATTAAGTATGTATATGTATTAAAAATTGAAATGAAAAATTATTTTATTAGTTTTTGAAATATTTTGGTATTATATTTAGAGGTGTTTGTG #<>> Writing bisulfite mapping results to EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1202:6821:3657_1:N:0:CGATGT Scaffold_09 2 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far 30015261 reads; of these: 30015261 (100.00%) were paired; of these: 18888567 (62.93%) aligned concordantly 0 times 5102104 (17.00%) aligned concordantly exactly 1 time 6024590 (20.07%) aligned concordantly >1 times 37.07% overall alignment rate 30015261 reads; of these: 30015261 (100.00%) were paired; of these: 18948145 (63.13%) aligned concordantly 0 times 5093125 (16.97%) aligned concordantly exactly 1 time 5973991 (19.90%) aligned concordantly >1 times 36.87% overall alignment rate Processed 30015261 sequences in total Successfully deleted the temporary files EPI-104_S28_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-104_S28_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 30015261 Number of paired-end alignments with a unique best hit: 13633936 Mapping efficiency: 45.4% Sequence pairs with no alignments under any condition: 13665400 Sequence pairs did not map uniquely: 2715925 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6781130 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6852805 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 418448650 Total methylated C's in CpG context: 15436769 Total methylated C's in CHG context: 2036052 Total methylated C's in CHH context: 3597610 Total methylated C's in Unknown context: 67853 Total unmethylated C's in CpG context: 41191940 Total unmethylated C's in CHG context: 85561381 Total unmethylated C's in CHH context: 270624898 Total unmethylated C's in Unknown context: 900361 C methylated in CpG context: 27.3% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 7.0% Bismark completed in 0d 1h 51m 52s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-111_S29_L005_R1_001_val_1.fq.gz to EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-111_S29_L005_R1_001_val_1.fq.gz (27014996 sequences in total) Writing a G -> A converted version of the input file EPI-111_S29_L005_R2_001_val_2.fq.gz to EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-111_S29_L005_R2_001_val_2.fq.gz (27014996 sequences in total) Input files are EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1222:1965_1:N:0:TTAGGC/1 99 Scaffold_02_CT_converted 52423574 6 101M = 52423755 280 NTGATGAGTGATTTATAATGTTTTGTAGGTTTATTAAAAGATTGTGTTTGTGTTTGTAATTTTTTTGATATATTGTTAATTAAAGTTGGGATGGTTGGATT #<>> Writing bisulfite mapping results to EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2305:8726:65045_1:N:0:TTAGGC Scaffold_14 2 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far 27014996 reads; of these: 27014996 (100.00%) were paired; of these: 16931638 (62.67%) aligned concordantly 0 times 4662317 (17.26%) aligned concordantly exactly 1 time 5421041 (20.07%) aligned concordantly >1 times 37.33% overall alignment rate 27014996 reads; of these: 27014996 (100.00%) were paired; of these: 17004362 (62.94%) aligned concordantly 0 times 4645643 (17.20%) aligned concordantly exactly 1 time 5364991 (19.86%) aligned concordantly >1 times 37.06% overall alignment rate Processed 27014996 sequences in total Successfully deleted the temporary files EPI-111_S29_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-111_S29_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27014996 Number of paired-end alignments with a unique best hit: 12312883 Mapping efficiency: 45.6% Sequence pairs with no alignments under any condition: 12235438 Sequence pairs did not map uniquely: 2466675 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6118719 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6194163 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 377453061 Total methylated C's in CpG context: 13097257 Total methylated C's in CHG context: 1893893 Total methylated C's in CHH context: 2999476 Total methylated C's in Unknown context: 59372 Total unmethylated C's in CpG context: 39327878 Total unmethylated C's in CHG context: 76742866 Total unmethylated C's in CHH context: 243391691 Total unmethylated C's in Unknown context: 784343 C methylated in CpG context: 25.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 7.0% Bismark completed in 0d 1h 40m 21s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-113_S30_L005_R1_001_val_1.fq.gz to EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-113_S30_L005_R1_001_val_1.fq.gz (26302191 sequences in total) Writing a G -> A converted version of the input file EPI-113_S30_L005_R2_001_val_2.fq.gz to EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-113_S30_L005_R2_001_val_2.fq.gz (26302191 sequences in total) Input files are EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1442:1956_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 NTAGTATTTTTATTAGAAGAATTAGAAATATTAGTAATAGTAAATTATTAGGTAGTGATAATATTGTAAATGAGTAATTAAAGTATTTATTATATGTGATG #>> Writing bisulfite mapping results to EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16931:96627_1:N:0:TGACCA Scaffold_13 44396777 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far 26302191 reads; of these: 26302191 (100.00%) were paired; of these: 16935818 (64.39%) aligned concordantly 0 times 4415733 (16.79%) aligned concordantly exactly 1 time 4950640 (18.82%) aligned concordantly >1 times 35.61% overall alignment rate 26302191 reads; of these: 26302191 (100.00%) were paired; of these: 17013134 (64.68%) aligned concordantly 0 times 4367646 (16.61%) aligned concordantly exactly 1 time 4921411 (18.71%) aligned concordantly >1 times 35.32% overall alignment rate Processed 26302191 sequences in total Successfully deleted the temporary files EPI-113_S30_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-113_S30_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 26302191 Number of paired-end alignments with a unique best hit: 11581686 Mapping efficiency: 44.0% Sequence pairs with no alignments under any condition: 12489960 Sequence pairs did not map uniquely: 2230545 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5744513 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5837172 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 359357698 Total methylated C's in CpG context: 12471829 Total methylated C's in CHG context: 1771590 Total methylated C's in CHH context: 2827755 Total methylated C's in Unknown context: 53715 Total unmethylated C's in CpG context: 37593518 Total unmethylated C's in CHG context: 73195958 Total unmethylated C's in CHH context: 231497048 Total unmethylated C's in Unknown context: 768555 C methylated in CpG context: 24.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.5% Bismark completed in 0d 1h 36m 39s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-119_S31_L005_R1_001_val_1.fq.gz to EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-119_S31_L005_R1_001_val_1.fq.gz (28905983 sequences in total) Writing a G -> A converted version of the input file EPI-119_S31_L005_R2_001_val_2.fq.gz to EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-119_S31_L005_R2_001_val_2.fq.gz (28905983 sequences in total) Input files are EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1132:1973_1:N:0:ACAGTG/1 99 Scaffold_12_CT_converted 4017483 2 93M = 4017483 -93 NTGGTGAAAATTTTGAAAATTGTTTAATAATGGTGTAAAATATTAATTTATATATTATTTTAGTAATTAGGGTGAAATATTTTGAAAGTAAGA #<>> Writing bisulfite mapping results to EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2302:14681:37197_1:N:0:ACAGTG Scaffold_16 2 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1304:7949:12013_1:N:0:ACAGTG Scaffold_16 2 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1215:10856:17476_1:N:0:ACAGTG Scaffold_16 2 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far 28905983 reads; of these: 28905983 (100.00%) were paired; of these: 19005598 (65.75%) aligned concordantly 0 times 4722302 (16.34%) aligned concordantly exactly 1 time 5178083 (17.91%) aligned concordantly >1 times 34.25% overall alignment rate 28905983 reads; of these: 28905983 (100.00%) were paired; of these: 19154447 (66.26%) aligned concordantly 0 times 4636303 (16.04%) aligned concordantly exactly 1 time 5115233 (17.70%) aligned concordantly >1 times 33.74% overall alignment rate Processed 28905983 sequences in total Successfully deleted the temporary files EPI-119_S31_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-119_S31_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28905983 Number of paired-end alignments with a unique best hit: 12331889 Mapping efficiency: 42.7% Sequence pairs with no alignments under any condition: 14292877 Sequence pairs did not map uniquely: 2281217 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6078960 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6252926 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 389840146 Total methylated C's in CpG context: 12477704 Total methylated C's in CHG context: 1827358 Total methylated C's in CHH context: 3035063 Total methylated C's in Unknown context: 49011 Total unmethylated C's in CpG context: 45041606 Total unmethylated C's in CHG context: 80081549 Total unmethylated C's in CHH context: 247376866 Total unmethylated C's in Unknown context: 795814 C methylated in CpG context: 21.7% C methylated in CHG context: 2.2% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 5.8% Bismark completed in 0d 1h 45m 41s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-120_S32_L005_R1_001_val_1.fq.gz to EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-120_S32_L005_R1_001_val_1.fq.gz (24140505 sequences in total) Writing a G -> A converted version of the input file EPI-120_S32_L005_R2_001_val_2.fq.gz to EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-120_S32_L005_R2_001_val_2.fq.gz (24140505 sequences in total) Input files are EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1140:1995_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 NGTATTTGGTTATATTTTAATATTAAATTTTGATTAAAATAGTTGTTGAAAATTGATTAGTATTATTTAGGAAGTATAGAAGTGTTAATATAAAGTTAATT #<>> Writing bisulfite mapping results to EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2203:1403:16239_1:N:0:GCCAAT Scaffold_09 2 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2110:13197:92900_1:N:0:GCCAAT Scaffold_09 3 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2102:12972:86705_1:N:0:GCCAAT Scaffold_09 2 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far 24140505 reads; of these: 24140505 (100.00%) were paired; of these: 15202444 (62.97%) aligned concordantly 0 times 4175808 (17.30%) aligned concordantly exactly 1 time 4762253 (19.73%) aligned concordantly >1 times 37.03% overall alignment rate 24140505 reads; of these: 24140505 (100.00%) were paired; of these: 15252082 (63.18%) aligned concordantly 0 times 4174115 (17.29%) aligned concordantly exactly 1 time 4714308 (19.53%) aligned concordantly >1 times 36.82% overall alignment rate Processed 24140505 sequences in total Successfully deleted the temporary files EPI-120_S32_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-120_S32_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24140505 Number of paired-end alignments with a unique best hit: 11050083 Mapping efficiency: 45.8% Sequence pairs with no alignments under any condition: 10973461 Sequence pairs did not map uniquely: 2116961 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5486119 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5563961 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 343610405 Total methylated C's in CpG context: 11964980 Total methylated C's in CHG context: 1672574 Total methylated C's in CHH context: 2746920 Total methylated C's in Unknown context: 46814 Total unmethylated C's in CpG context: 35958013 Total unmethylated C's in CHG context: 69824544 Total unmethylated C's in CHH context: 221443374 Total unmethylated C's in Unknown context: 719473 C methylated in CpG context: 25.0% C methylated in CHG context: 2.3% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.1% Bismark completed in 0d 1h 37m 34s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-127_S33_L005_R1_001_val_1.fq.gz to EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-127_S33_L005_R1_001_val_1.fq.gz (22262118 sequences in total) Writing a G -> A converted version of the input file EPI-127_S33_L005_R2_001_val_2.fq.gz to EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-127_S33_L005_R2_001_val_2.fq.gz (22262118 sequences in total) Input files are EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1259:1963_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 NTATTTATTTTTATATATTATTAAAAATTTATATTTTTATTATTAAAAATATAAATTTATATATTATTAATAATTTATTTTTATATTTTATTAATAAT #<>> Writing bisulfite mapping results to EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2302:15297:83758_1:N:0:CAGATC Scaffold_09 1 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far 22262118 reads; of these: 22262118 (100.00%) were paired; of these: 14211965 (63.84%) aligned concordantly 0 times 3770814 (16.94%) aligned concordantly exactly 1 time 4279339 (19.22%) aligned concordantly >1 times 36.16% overall alignment rate 22262118 reads; of these: 22262118 (100.00%) were paired; of these: 14293314 (64.20%) aligned concordantly 0 times 3750672 (16.85%) aligned concordantly exactly 1 time 4218132 (18.95%) aligned concordantly >1 times 35.80% overall alignment rate Processed 22262118 sequences in total Successfully deleted the temporary files EPI-127_S33_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-127_S33_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22262118 Number of paired-end alignments with a unique best hit: 9986595 Mapping efficiency: 44.9% Sequence pairs with no alignments under any condition: 10417464 Sequence pairs did not map uniquely: 1858059 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4954421 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5032173 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 314010295 Total methylated C's in CpG context: 11042968 Total methylated C's in CHG context: 1520028 Total methylated C's in CHH context: 2541364 Total methylated C's in Unknown context: 47519 Total unmethylated C's in CpG context: 33055152 Total unmethylated C's in CHG context: 64128787 Total unmethylated C's in CHH context: 201721996 Total unmethylated C's in Unknown context: 647317 C methylated in CpG context: 25.0% C methylated in CHG context: 2.3% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.8% Bismark completed in 0d 1h 30m 4s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-128_S34_L005_R1_001_val_1.fq.gz to EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-128_S34_L005_R1_001_val_1.fq.gz (24557803 sequences in total) Writing a G -> A converted version of the input file EPI-128_S34_L005_R2_001_val_2.fq.gz to EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-128_S34_L005_R2_001_val_2.fq.gz (24557803 sequences in total) Input files are EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1617:1971_1:N:0:ACTTGA/1 99 Scaffold_07_CT_converted 39044038 2 98M = 39044221 281 NGAGATTATTTAATATAGATATGTGTTTAAGGTTTTGGTAGATATTGTTAATTATGATTATTGAGGTTATTTAATATAGATATGTTTTAAAGGTTTGG #<<>> Writing bisulfite mapping results to EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2107:9857:95864_1:N:0:ACTTGA Scaffold_16 2 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1116:4355:21006_1:N:0:ACTTGA Scaffold_16 2 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far 24557803 reads; of these: 24557803 (100.00%) were paired; of these: 15716613 (64.00%) aligned concordantly 0 times 4172368 (16.99%) aligned concordantly exactly 1 time 4668822 (19.01%) aligned concordantly >1 times 36.00% overall alignment rate 24557803 reads; of these: 24557803 (100.00%) were paired; of these: 15638441 (63.68%) aligned concordantly 0 times 4202494 (17.11%) aligned concordantly exactly 1 time 4716868 (19.21%) aligned concordantly >1 times 36.32% overall alignment rate Processed 24557803 sequences in total Successfully deleted the temporary files EPI-128_S34_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-128_S34_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24557803 Number of paired-end alignments with a unique best hit: 11023912 Mapping efficiency: 44.9% Sequence pairs with no alignments under any condition: 11430018 Sequence pairs did not map uniquely: 2103873 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5468345 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5555565 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 342815591 Total methylated C's in CpG context: 12084385 Total methylated C's in CHG context: 1712206 Total methylated C's in CHH context: 2665031 Total methylated C's in Unknown context: 47752 Total unmethylated C's in CpG context: 36262181 Total unmethylated C's in CHG context: 69681804 Total unmethylated C's in CHH context: 220409984 Total unmethylated C's in Unknown context: 723863 C methylated in CpG context: 25.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.2% Bismark completed in 0d 1h 37m 45s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-135_S35_L005_R1_001_val_1.fq.gz to EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-135_S35_L005_R1_001_val_1.fq.gz (28731808 sequences in total) Writing a G -> A converted version of the input file EPI-135_S35_L005_R2_001_val_2.fq.gz to EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-135_S35_L005_R2_001_val_2.fq.gz (28731808 sequences in total) Input files are EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1469:1995_1:N:0:GATCAG/1 99 Scaffold_02_CT_converted 52412008 1 97M = 52412014 104 NTGTATTTGTTATATTTTTAAAATAAATTAAAATTTTAATTATTTGTTTATTTTGTTTTTTTGGAATTTTGAGTGTATATGTATTATATAATTTATT #<>> Writing bisulfite mapping results to EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1106:4844:54933_1:N:0:GATCAG Scaffold_16 2 Processed 28000000 sequence pairs so far 28731808 reads; of these: 28731808 (100.00%) were paired; of these: 18174330 (63.26%) aligned concordantly 0 times 4818195 (16.77%) aligned concordantly exactly 1 time 5739283 (19.98%) aligned concordantly >1 times 36.74% overall alignment rate 28731808 reads; of these: 28731808 (100.00%) were paired; of these: 18095326 (62.98%) aligned concordantly 0 times 4833538 (16.82%) aligned concordantly exactly 1 time 5802944 (20.20%) aligned concordantly >1 times 37.02% overall alignment rate Processed 28731808 sequences in total Successfully deleted the temporary files EPI-135_S35_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-135_S35_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28731808 Number of paired-end alignments with a unique best hit: 12720631 Mapping efficiency: 44.3% Sequence pairs with no alignments under any condition: 13210078 Sequence pairs did not map uniquely: 2801099 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6307893 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6412737 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 379885177 Total methylated C's in CpG context: 14174074 Total methylated C's in CHG context: 2097825 Total methylated C's in CHH context: 3204273 Total methylated C's in Unknown context: 64166 Total unmethylated C's in CpG context: 39497431 Total unmethylated C's in CHG context: 77915331 Total unmethylated C's in CHH context: 242996243 Total unmethylated C's in Unknown context: 785379 C methylated in CpG context: 26.4% C methylated in CHG context: 2.6% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 7.6% Bismark completed in 0d 1h 48m 58s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-136_S36_L005_R1_001_val_1.fq.gz to EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-136_S36_L005_R1_001_val_1.fq.gz (27792315 sequences in total) Writing a G -> A converted version of the input file EPI-136_S36_L005_R2_001_val_2.fq.gz to EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-136_S36_L005_R2_001_val_2.fq.gz (27792315 sequences in total) Input files are EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1242:1980_1:N:0:TAGCTT/1 99 Scaffold_11_CT_converted 30489349 0 100M = 30489366 109 NATGGTTGGATTATTTTATAGTTAAAATATTATGAGGTGTATTGATTGTTTTATTTTGAGATGTTGTGTAGATATTGTTTTAATGGGGTGTAGTGTTTTT #<>> Writing bisulfite mapping results to EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1205:15387:22738_1:N:0:TAGCTT Scaffold_13 44396778 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far 27792315 reads; of these: 27792315 (100.00%) were paired; of these: 17640819 (63.47%) aligned concordantly 0 times 4583263 (16.49%) aligned concordantly exactly 1 time 5568233 (20.04%) aligned concordantly >1 times 36.53% overall alignment rate 27792315 reads; of these: 27792315 (100.00%) were paired; of these: 17566832 (63.21%) aligned concordantly 0 times 4600321 (16.55%) aligned concordantly exactly 1 time 5625162 (20.24%) aligned concordantly >1 times 36.79% overall alignment rate Processed 27792315 sequences in total Successfully deleted the temporary files EPI-136_S36_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-136_S36_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27792315 Number of paired-end alignments with a unique best hit: 12229034 Mapping efficiency: 44.0% Sequence pairs with no alignments under any condition: 12912342 Sequence pairs did not map uniquely: 2650939 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6066303 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6162730 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 371098859 Total methylated C's in CpG context: 12526554 Total methylated C's in CHG context: 1883224 Total methylated C's in CHH context: 2923602 Total methylated C's in Unknown context: 54090 Total unmethylated C's in CpG context: 39735089 Total unmethylated C's in CHG context: 76137777 Total unmethylated C's in CHH context: 237892613 Total unmethylated C's in Unknown context: 810936 C methylated in CpG context: 24.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.3% Bismark completed in 0d 1h 59m 35s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-143_S37_L005_R1_001_val_1.fq.gz to EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-143_S37_L005_R1_001_val_1.fq.gz (21160872 sequences in total) Writing a G -> A converted version of the input file EPI-143_S37_L005_R2_001_val_2.fq.gz to EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-143_S37_L005_R2_001_val_2.fq.gz (21160872 sequences in total) Input files are EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1205:1956_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 NGAAGGAAAATGAATTGATAGTATTATAAGGTTTAAATTTGTTATTATTTTTATAATTTGTATTATTTTTATTATTATGTTATATTTTTATAAATAAATTT #<>> Writing bisulfite mapping results to EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2115:10166:97532_1:N:0:GGCTAC Scaffold_09 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far 21160872 reads; of these:21160872 reads; of these: 21160872 (21160872 (100.00100.00%%) were paired; of these:) were paired; of these: 1364908413590247 ( (64.5064.22%%) aligned concordantly 0 times) aligned concordantly 0 times 35112973523727 ( (16.5916.65%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 40004914046898 ( (18.9119.12%%) aligned concordantly >1 times) aligned concordantly >1 times 35.5035.78%% overall alignment rate overall alignment rate Processed 21160872 sequences in total Successfully deleted the temporary files EPI-143_S37_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-143_S37_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 21160872 Number of paired-end alignments with a unique best hit: 9316819 Mapping efficiency: 44.0% Sequence pairs with no alignments under any condition: 10036514 Sequence pairs did not map uniquely: 1807539 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4624000 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4692818 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 288290011 Total methylated C's in CpG context: 10342749 Total methylated C's in CHG context: 1387455 Total methylated C's in CHH context: 2413979 Total methylated C's in Unknown context: 44158 Total unmethylated C's in CpG context: 29588909 Total unmethylated C's in CHG context: 58728884 Total unmethylated C's in CHH context: 185828035 Total unmethylated C's in Unknown context: 610790 C methylated in CpG context: 25.9% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 6.7% Bismark completed in 0d 1h 21m 14s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-145_S38_L005_R1_001_val_1.fq.gz to EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-145_S38_L005_R1_001_val_1.fq.gz (25314513 sequences in total) Writing a G -> A converted version of the input file EPI-145_S38_L005_R2_001_val_2.fq.gz to EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-145_S38_L005_R2_001_val_2.fq.gz (25314513 sequences in total) Input files are EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1386:1965_1:N:0:CTTGTA/1 99 Scaffold_01_CT_converted 61447290 40 97M = 61447296 105 NTGGGTAAGTAAAGATATAATATTGTAAGTATTATTATGTATATAAGTTTTATATTTTTTTTTTGAGGGTTGAAGTGTTATTATTTTGATATATATT #<>> Writing bisulfite mapping results to EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2203:7305:92572_1:N:0:CTTGTA Scaffold_16 3 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:1106:12531:67820_1:N:0:CTTGTA Scaffold_16 1 Processed 25000000 sequence pairs so far 25314513 reads; of these: 25314513 (100.00%) were paired; of these: 16271826 (64.28%) aligned concordantly 0 times 4267243 (16.86%) aligned concordantly exactly 1 time 4775444 (18.86%) aligned concordantly >1 times 35.72% overall alignment rate 25314513 reads; of these: 25314513 (100.00%) were paired; of these: 16361226 (64.63%) aligned concordantly 0 times 4230313 (16.71%) aligned concordantly exactly 1 time 4722974 (18.66%) aligned concordantly >1 times 35.37% overall alignment rate Processed 25314513 sequences in total Successfully deleted the temporary files EPI-145_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-145_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 25314513 Number of paired-end alignments with a unique best hit: 11191276 Mapping efficiency: 44.2% Sequence pairs with no alignments under any condition: 11992514 Sequence pairs did not map uniquely: 2130723 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5539947 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5651327 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 346932784 Total methylated C's in CpG context: 12322055 Total methylated C's in CHG context: 1693840 Total methylated C's in CHH context: 2773795 Total methylated C's in Unknown context: 48529 Total unmethylated C's in CpG context: 36498527 Total unmethylated C's in CHG context: 70595301 Total unmethylated C's in CHH context: 223049266 Total unmethylated C's in Unknown context: 722709 C methylated in CpG context: 25.2% C methylated in CHG context: 2.3% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.3% Bismark completed in 0d 1h 36m 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-151_S2_L002_R1_001_val_1.fq.gz to EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-151_S2_L002_R1_001_val_1.fq.gz (24505793 sequences in total) Writing a G -> A converted version of the input file EPI-151_S2_L002_R2_001_val_2.fq.gz to EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-151_S2_L002_R2_001_val_2.fq.gz (24505793 sequences in total) Input files are EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_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/v01/ 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-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_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:2:2207:1928:2248_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TAGTAGAGGTTTATATGTATTTATGTTTGGTTAGAAAAGGTTTATATGTATTTATGTTTGGTTAGTAGAGGTTTATATGTATTTATGTTTGGTTA BBBBBFFBFFBBFBBBBFFF/B/FBBF>> Writing bisulfite mapping results to EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2114:2329:9695_1:N:0:ATCACG Scaffold_09 2 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 24505793 reads; of these: 24505793 (100.00%) were paired; of these: 16362174 (66.77%) aligned concordantly 0 times 3586050 (14.63%) aligned concordantly exactly 1 time 4557569 (18.60%) aligned concordantly >1 times 33.23% overall alignment rate 24505793 reads; of these: 24505793 (100.00%) were paired; of these: 16471528 (67.21%) aligned concordantly 0 times 3553354 (14.50%) aligned concordantly exactly 1 time 4480911 (18.29%) aligned concordantly >1 times 32.79% overall alignment rate Processed 24505793 sequences in total Successfully deleted the temporary files EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24505793 Number of paired-end alignments with a unique best hit: 9915442 Mapping efficiency: 40.5% Sequence pairs with no alignments under any condition: 12555282 Sequence pairs did not map uniquely: 2035069 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: 4881878 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5033563 ((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: 303264962 Total methylated C's in CpG context: 12323211 Total methylated C's in CHG context: 1414630 Total methylated C's in CHH context: 3533701 Total methylated C's in Unknown context: 52135 Total unmethylated C's in CpG context: 31194293 Total unmethylated C's in CHG context: 65160946 Total unmethylated C's in CHH context: 189638181 Total unmethylated C's in Unknown context: 646387 C methylated in CpG context: 28.3% C methylated in CHG context: 2.1% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 7.5% Bismark completed in 0d 1h 24m 28s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-152_S3_L002_R1_001_val_1.fq.gz to EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-152_S3_L002_R1_001_val_1.fq.gz (29855018 sequences in total) Writing a G -> A converted version of the input file EPI-152_S3_L002_R2_001_val_2.fq.gz to EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-152_S3_L002_R2_001_val_2.fq.gz (29855018 sequences in total) Input files are EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_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/v01/ 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-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_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:2:2207:1155:2233_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 AATGGNTATGAAAATGTAATAAAGGAAGAGATATGAAAATGTAATAAAGGAANATTTATGANAATGTATTGTGGGAAGTGATATGAAAATGTAATATG BBBBB#B>> Writing bisulfite mapping results to EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_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 29855018 reads; of these: 29855018 (100.00%) were paired; of these: 20215536 (67.71%) aligned concordantly 0 times 4311215 (14.44%) aligned concordantly exactly 1 time 5328267 (17.85%) aligned concordantly >1 times 32.29% overall alignment rate 29855018 reads; of these: 29855018 (100.00%) were paired; of these: 20302194 (68.00%) aligned concordantly 0 times 4294798 (14.39%) aligned concordantly exactly 1 time 5258026 (17.61%) aligned concordantly >1 times 32.00% overall alignment rate Processed 29855018 sequences in total Successfully deleted the temporary files EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29855018 Number of paired-end alignments with a unique best hit: 11727816 Mapping efficiency: 39.3% Sequence pairs with no alignments under any condition: 15750735 Sequence pairs did not map uniquely: 2376467 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: 5811638 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5916178 ((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: 358780662 Total methylated C's in CpG context: 14625118 Total methylated C's in CHG context: 1782524 Total methylated C's in CHH context: 4106805 Total methylated C's in Unknown context: 73648 Total unmethylated C's in CpG context: 34864391 Total unmethylated C's in CHG context: 74934034 Total unmethylated C's in CHH context: 228467790 Total unmethylated C's in Unknown context: 784418 C methylated in CpG context: 29.6% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 8.6% Bismark completed in 0d 1h 37m 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-153_S4_L002_R1_001_val_1.fq.gz to EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-153_S4_L002_R1_001_val_1.fq.gz (26009397 sequences in total) Writing a G -> A converted version of the input file EPI-153_S4_L002_R2_001_val_2.fq.gz to EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-153_S4_L002_R2_001_val_2.fq.gz (26009397 sequences in total) Input files are EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_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/v01/ 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-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_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:2:2207:1785:2231_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 TGTTGNGATATATAATTGAAAATTGTTGAAAGTGTTATTAAATATAATGTAATAATAAATGATAAAGGGATGTAATGTTGTATATTAATTATTAT BBBBB#BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:2:2207:1785:2231_2:N:0:TTAGGC/2 141 * 0 0 * * 0 0 ATANNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNATTTATTATTACATTATATTTAATAACACTTTCAACAATTTTCAATTATATATCACAACA BBB############################B###BB<>> Writing bisulfite mapping results to EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1115:15676:64681_1:N:0:TTAGGC Scaffold_08 61151067 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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2314:20445:24921_1:N:0:TTAGGC Scaffold_11 1 Processed 26000000 sequence pairs so far 26009397 reads; of these: 26009397 reads; of these:26009397 ( 26009397 (100.00%) were paired; of these:100.00 % ) were paired; of these:17345929 ( 66.6917425568% () aligned concordantly 0 times67.00 % ) aligned concordantly 0 times3790523 ( 14.573786588% () aligned concordantly exactly 1 time14.56 % ) aligned concordantly exactly 1 time4872945 ( 18.744797241% () aligned concordantly >1 times18.44 %33.31) aligned concordantly >1 times% overall alignment rate33.00 % overall alignment rate Processed 26009397 sequences in total Successfully deleted the temporary files EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 26009397 Number of paired-end alignments with a unique best hit: 10439073 Mapping efficiency: 40.1% Sequence pairs with no alignments under any condition: 13324084 Sequence pairs did not map uniquely: 2246240 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: 5162472 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5276599 ((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: 313246619 Total methylated C's in CpG context: 12166335 Total methylated C's in CHG context: 1553054 Total methylated C's in CHH context: 3545799 Total methylated C's in Unknown context: 59307 Total unmethylated C's in CpG context: 33102077 Total unmethylated C's in CHG context: 67300222 Total unmethylated C's in CHH context: 195579132 Total unmethylated C's in Unknown context: 676779 C methylated in CpG context: 26.9% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 8.1% Bismark completed in 0d 1h 27m 52s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-154_S5_L002_R1_001_val_1.fq.gz to EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-154_S5_L002_R1_001_val_1.fq.gz (25226760 sequences in total) Writing a G -> A converted version of the input file EPI-154_S5_L002_R2_001_val_2.fq.gz to EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-154_S5_L002_R2_001_val_2.fq.gz (25226760 sequences in total) Input files are EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_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/v01/ 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-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_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:2:2207:2191:2242_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 ATGTANATTAAGAGTTAAATTATGTAGATGTAGATTAAAAGTTAAATTATGTATAGGTAGATTAAGAGTTAAATTAAGTAGATGTAGATTAAGAGTTTAAT BBBBB#>> Writing bisulfite mapping results to EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_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 25226760 reads; of these: 25226760 (100.00%) were paired; of these: 17487663 (69.32%) aligned concordantly 0 times 3441962 (13.64%) aligned concordantly exactly 1 time 4297135 (17.03%) aligned concordantly >1 times 30.68% overall alignment rate 25226760 reads; of these: 25226760 (100.00%) were paired; of these: 17561189 (69.61%) aligned concordantly 0 times 3444557 (13.65%) aligned concordantly exactly 1 time 4221014 (16.73%) aligned concordantly >1 times 30.39% overall alignment rate Processed 25226760 sequences in total Successfully deleted the temporary files EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 25226760 Number of paired-end alignments with a unique best hit: 9405544 Mapping efficiency: 37.3% Sequence pairs with no alignments under any condition: 13904236 Sequence pairs did not map uniquely: 1916980 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: 4637602 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4767942 ((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: 285373397 Total methylated C's in CpG context: 11306006 Total methylated C's in CHG context: 1298778 Total methylated C's in CHH context: 3449101 Total methylated C's in Unknown context: 62682 Total unmethylated C's in CpG context: 28242299 Total unmethylated C's in CHG context: 60128621 Total unmethylated C's in CHH context: 180948592 Total unmethylated C's in Unknown context: 625876 C methylated in CpG context: 28.6% C methylated in CHG context: 2.1% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 9.1% Bismark completed in 0d 1h 24m 24s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-159_S6_L002_R1_001_val_1.fq.gz to EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-159_S6_L002_R1_001_val_1.fq.gz (15453987 sequences in total) Writing a G -> A converted version of the input file EPI-159_S6_L002_R2_001_val_2.fq.gz to EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-159_S6_L002_R2_001_val_2.fq.gz (15453987 sequences in total) Input files are EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_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/v01/ 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-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_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:2:2207:1469:2230_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 GGTTANTGAAGTGTATATAGTTATATTGTAAATTAATGGTTGAGTGAGTTTTNTTTTTTATTAGGTAATATTTTAAGGGAATGGTTGTTTGTAAATATTGG BBBBB#BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFF#<>> Writing bisulfite mapping results to EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_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 15453987 reads; of these: 15453987 (100.00%) were paired; of these: 10221296 (66.14%) aligned concordantly 0 times 2334749 (15.11%) aligned concordantly exactly 1 time 2897942 (18.75%) aligned concordantly >1 times 33.86% overall alignment rate 15453987 reads; of these: 15453987 (100.00%) were paired; of these: 10169665 (65.81%) aligned concordantly 0 times 2347488 (15.19%) aligned concordantly exactly 1 time 2936834 (19.00%) aligned concordantly >1 times 34.19% overall alignment rate Processed 15453987 sequences in total Successfully deleted the temporary files EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 15453987 Number of paired-end alignments with a unique best hit: 6380873 Mapping efficiency: 41.3% Sequence pairs with no alignments under any condition: 7739907 Sequence pairs did not map uniquely: 1333207 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: 3152381 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3228492 ((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: 195385696 Total methylated C's in CpG context: 7804592 Total methylated C's in CHG context: 1021997 Total methylated C's in CHH context: 3443697 Total methylated C's in Unknown context: 54626 Total unmethylated C's in CpG context: 19140558 Total unmethylated C's in CHG context: 40545239 Total unmethylated C's in CHH context: 123429613 Total unmethylated C's in Unknown context: 431888 C methylated in CpG context: 29.0% C methylated in CHG context: 2.5% C methylated in CHH context: 2.7% C methylated in unknown context (CN or CHN): 11.2% Bismark completed in 0d 0h 57m 50s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-160_S7_L002_R1_001_val_1.fq.gz to EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-160_S7_L002_R1_001_val_1.fq.gz (31922572 sequences in total) Writing a G -> A converted version of the input file EPI-160_S7_L002_R2_001_val_2.fq.gz to EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-160_S7_L002_R2_001_val_2.fq.gz (31922572 sequences in total) Input files are EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_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/v01/ 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-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_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:2:2207:1522:2231_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 GTATGNGTAATTAGGTGATTTTTTTTGATTTGATGTAGTTAGTGGATTGGGAATTGGTAA BBBBB#BBBFFBFFFFFFFFFFFFFFB/>> Writing bisulfite mapping results to EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1114:12011:63361_1:N:0:GCCAAT Scaffold_16 2 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 31922572 reads; of these: 31922572 (100.00%) were paired; of these: 21498211 (67.34%) aligned concordantly 0 times 4482845 (14.04%) aligned concordantly exactly 1 time 5941516 (18.61%31922572) aligned concordantly >1 times reads; of these: 32.66 %31922572 overall alignment rate ( 100.00%) were paired; of these: 21367255 (66.93%) aligned concordantly 0 times 4496752 (14.09%) aligned concordantly exactly 1 time 6058565 (18.98%) aligned concordantly >1 times 33.07% overall alignment rate Processed 31922572 sequences in total Successfully deleted the temporary files EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 31922572 Number of paired-end alignments with a unique best hit: 12255649 Mapping efficiency: 38.4% Sequence pairs with no alignments under any condition: 16675995 Sequence pairs did not map uniquely: 2990928 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: 6034016 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6221632 ((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: 356119849 Total methylated C's in CpG context: 13819770 Total methylated C's in CHG context: 1872039 Total methylated C's in CHH context: 4292886 Total methylated C's in Unknown context: 84309 Total unmethylated C's in CpG context: 37264731 Total unmethylated C's in CHG context: 75867945 Total unmethylated C's in CHH context: 223002478 Total unmethylated C's in Unknown context: 787408 C methylated in CpG context: 27.1% C methylated in CHG context: 2.4% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 9.7% Bismark completed in 0d 1h 45m 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-161_S8_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-161_S8_L002_R1_001_val_1.fq.gz to EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-161_S8_L002_R1_001_val_1.fq.gz (24510805 sequences in total) Writing a G -> A converted version of the input file EPI-161_S8_L002_R2_001_val_2.fq.gz to EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-161_S8_L002_R2_001_val_2.fq.gz (24510805 sequences in total) Input files are EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_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/v01/ 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-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_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:2:2207:2010:2229_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TGATANGTAGTATATGGTGTATGATATAGTA BBBBB#>> Writing bisulfite mapping results to EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2114:19616:68633_1:N:0:CAGATC Scaffold_16 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1112:4795:6211_1:N:0:CAGATC Scaffold_16 2 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 24510805 reads; of these: 24510805 (24510805 reads; of these: 24510805 (100.00%) were paired; of these:100.00 % ) were paired; of these:17217869 ( 70.2517297281% () aligned concordantly 0 times70.57 % ) aligned concordantly 0 times3175317 ( 12.953166248% () aligned concordantly exactly 1 time12.92 % ) aligned concordantly exactly 1 time4117619 ( 404727616.80 (%16.51) aligned concordantly >1 times% ) aligned concordantly >1 times29.75 %29.43 overall alignment rate% overall alignment rate Processed 24510805 sequences in total Successfully deleted the temporary files EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24510805 Number of paired-end alignments with a unique best hit: 8593707 Mapping efficiency: 35.1% Sequence pairs with no alignments under any condition: 13929047 Sequence pairs did not map uniquely: 1988051 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: 4237007 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4356698 ((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: 251244640 Total methylated C's in CpG context: 9311185 Total methylated C's in CHG context: 1241250 Total methylated C's in CHH context: 3334595 Total methylated C's in Unknown context: 63649 Total unmethylated C's in CpG context: 25878911 Total unmethylated C's in CHG context: 52710364 Total unmethylated C's in CHH context: 158768335 Total unmethylated C's in Unknown context: 546831 C methylated in CpG context: 26.5% C methylated in CHG context: 2.3% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 10.4% Bismark completed in 0d 1h 12m 12s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-162_S9_L002_R1_001_val_1.fq.gz to EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-162_S9_L002_R1_001_val_1.fq.gz (22769546 sequences in total) Writing a G -> A converted version of the input file EPI-162_S9_L002_R2_001_val_2.fq.gz to EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-162_S9_L002_R2_001_val_2.fq.gz (22769546 sequences in total) Input files are EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_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/v01/ 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-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_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:2:2207:1238:2233_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 TGTTANTTATTTTAAAATTTGTTGATAAATTGTTTATTTTTAGGATAGTTTTTTTAGATATTGTTTTTTTTTGGTTTGAAAGGGTTATGAATAGTTTTTTT BBBBB#>> Writing bisulfite mapping results to EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_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 22769546 reads; of these: 22769546 (100.00%) were paired; of these: 15616786 (68.59%) aligned concordantly 0 times 3009100 (13.22%) aligned concordantly exactly 1 time 4143660 (18.20%) aligned concordantly >1 times 31.41% overall alignment rate 22769546 reads; of these: 22769546 (100.00%) were paired; of these: 15681883 (68.87%) aligned concordantly 0 times 3024375 (13.28%) aligned concordantly exactly 1 time 4063288 (17.85%) aligned concordantly >1 times 31.13% overall alignment rate Processed 22769546 sequences in total Successfully deleted the temporary files EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22769546 Number of paired-end alignments with a unique best hit: 8267039 Mapping efficiency: 36.3% Sequence pairs with no alignments under any condition: 12467371 Sequence pairs did not map uniquely: 2035136 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: 4073674 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4193365 ((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: 238005650 Total methylated C's in CpG context: 8810888 Total methylated C's in CHG context: 1190010 Total methylated C's in CHH context: 3285737 Total methylated C's in Unknown context: 56519 Total unmethylated C's in CpG context: 24654378 Total unmethylated C's in CHG context: 50555362 Total unmethylated C's in CHH context: 149509275 Total unmethylated C's in Unknown context: 528637 C methylated in CpG context: 26.3% C methylated in CHG context: 2.3% C methylated in CHH context: 2.2% C methylated in unknown context (CN or CHN): 9.7% Bismark completed in 0d 1h 7m 57s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-167_S10_L002_R1_001_val_1.fq.gz to EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-167_S10_L002_R1_001_val_1.fq.gz (24481250 sequences in total) Writing a G -> A converted version of the input file EPI-167_S10_L002_R2_001_val_2.fq.gz to EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-167_S10_L002_R2_001_val_2.fq.gz (24481250 sequences in total) Input files are EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_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/v01/ 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-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_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:2:2207:1666:2232_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 TTGAANTTGTTGATTTATATGGGGATATGAATAATAAGTTTAATATTTAAGATGGAGAAGAAATAAGTGTAGAATTTTGGATAAAGGATAATTAAGTTAAT BBBBB#BBFFFFFF>> Writing bisulfite mapping results to EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_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 24481250 reads; of these: 24481250 (100.00%) were paired; of these: 16118278 (65.84%) aligned concordantly 0 times 3811968 (15.57%) aligned concordantly exactly 1 time 4551004 (18.59%) aligned concordantly >1 times 34.16% overall alignment rate 24481250 reads; of these: 24481250 (100.00%) were paired; of these: 16050656 (65.56%) aligned concordantly 0 times 3801758 (15.53%) aligned concordantly exactly 1 time 4628836 (18.91%) aligned concordantly >1 times 34.44% overall alignment rate Processed 24481250 sequences in total Successfully deleted the temporary files EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 24481250 Number of paired-end alignments with a unique best hit: 10438000 Mapping efficiency: 42.6% Sequence pairs with no alignments under any condition: 12046563 Sequence pairs did not map uniquely: 1996687 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: 5166645 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5271355 ((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: 327276929 Total methylated C's in CpG context: 12357096 Total methylated C's in CHG context: 2047643 Total methylated C's in CHH context: 6308688 Total methylated C's in Unknown context: 65277 Total unmethylated C's in CpG context: 31908920 Total unmethylated C's in CHG context: 67977563 Total unmethylated C's in CHH context: 206677019 Total unmethylated C's in Unknown context: 705078 C methylated in CpG context: 27.9% C methylated in CHG context: 2.9% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 8.5% Bismark completed in 0d 1h 26m 47s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-168_S11_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-168_S11_L002_R1_001_val_1.fq.gz to EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-168_S11_L002_R1_001_val_1.fq.gz (22688467 sequences in total) Writing a G -> A converted version of the input file EPI-168_S11_L002_R2_001_val_2.fq.gz to EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-168_S11_L002_R2_001_val_2.fq.gz (22688467 sequences in total) Input files are EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_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/v01/ 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-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_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:2:2207:1424:2239_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 GTGATNTATAATGTATTATTGAAAGTTAATAGTTTATTTAAGTTTTTGGTATTTTTTGATTTAGGTTTAATTATTTTGTTATGTGGGTTTGTGATTTG BBBBB#B>> Writing bisulfite mapping results to EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_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 22688467 reads; of these: 22688467 (100.00%) were paired; of these: 15440681 (68.06%) aligned concordantly 0 times 3190562 (14.06%) aligned concordantly exactly 1 time 4057224 (17.88%) aligned concordantly >1 times 31.94% overall alignment rate 22688467 reads; of these: 22688467 (100.00%) were paired; of these: 15321747 (67.53%) aligned concordantly 0 times 3226165 (14.22%) aligned concordantly exactly 1 time 4140555 (18.25%) aligned concordantly >1 times 32.47% overall alignment rate Processed 22688467 sequences in total Successfully deleted the temporary files EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22688467 Number of paired-end alignments with a unique best hit: 8967128 Mapping efficiency: 39.5% Sequence pairs with no alignments under any condition: 11891374 Sequence pairs did not map uniquely: 1829965 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: 4393790 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4573338 ((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: 278794431 Total methylated C's in CpG context: 10658385 Total methylated C's in CHG context: 1268483 Total methylated C's in CHH context: 3535297 Total methylated C's in Unknown context: 54743 Total unmethylated C's in CpG context: 29012483 Total unmethylated C's in CHG context: 59889529 Total unmethylated C's in CHH context: 174430254 Total unmethylated C's in Unknown context: 615881 C methylated in CpG context: 26.9% C methylated in CHG context: 2.1% C methylated in CHH context: 2.0% C methylated in unknown context (CN or CHN): 8.2% Bismark completed in 0d 1h 14m 52s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-169_S12_L002_R1_001_val_1.fq.gz to EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-169_S12_L002_R1_001_val_1.fq.gz (21392200 sequences in total) Writing a G -> A converted version of the input file EPI-169_S12_L002_R2_001_val_2.fq.gz to EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-169_S12_L002_R2_001_val_2.fq.gz (21392200 sequences in total) Input files are EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_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/v01/ 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-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_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:2:2207:1452:2231_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 TGGTANGAGGTTGTGTGATTAGTATAAAGGTGTTTAGAGTTATTAAGTGGATTGGATTGGAGTTTGGATTGGTTTTGTATTAATAAAAGTGTTTTTTTTGT BBBBB#<>> Writing bisulfite mapping results to EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2205:7072:26521_1:N:0:GGCTAC Scaffold_09 1 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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1306:7118:3504_1:N:0:GGCTAC Scaffold_16 2 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:2:1208:9887:13727_1:N:0:GGCTAC Scaffold_16 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1114:15881:53162_1:N:0:GGCTAC Scaffold_10 1 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 21392200 reads; of these: 21392200 (100.00%) were paired; of these: 14178782 (66.28%) aligned concordantly 0 times 3054776 (14.28%) aligned concordantly exactly 1 time 4158642 (19.44%) aligned concordantly >1 times 33.72% overall alignment rate 21392200 reads; of these: 21392200 (100.00%) were paired; of these: 14275451 (66.73%) aligned concordantly 0 times 3039394 (14.21%) aligned concordantly exactly 1 time 4077355 (19.06%) aligned concordantly >1 times 33.27% overall alignment rate Processed 21392200 sequences in total Successfully deleted the temporary files EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 21392200 Number of paired-end alignments with a unique best hit: 8408059 Mapping efficiency: 39.3% Sequence pairs with no alignments under any condition: 10932504 Sequence pairs did not map uniquely: 2051637 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: 4126394 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4281661 ((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: 245148711 Total methylated C's in CpG context: 9715161 Total methylated C's in CHG context: 1293014 Total methylated C's in CHH context: 3765782 Total methylated C's in Unknown context: 64209 Total unmethylated C's in CpG context: 25600954 Total unmethylated C's in CHG context: 52728521 Total unmethylated C's in CHH context: 152045279 Total unmethylated C's in Unknown context: 533680 C methylated in CpG context: 27.5% C methylated in CHG context: 2.4% C methylated in CHH context: 2.4% C methylated in unknown context (CN or CHN): 10.7% Bismark completed in 0d 1h 8m 11s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-170_S13_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-170_S13_L002_R1_001_val_1.fq.gz to EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-170_S13_L002_R1_001_val_1.fq.gz (27996279 sequences in total) Writing a G -> A converted version of the input file EPI-170_S13_L002_R2_001_val_2.fq.gz to EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-170_S13_L002_R2_001_val_2.fq.gz (27996279 sequences in total) Input files are EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_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/v01/ 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-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_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:2:2207:2244:2228_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 TTGTTNAGTTTGTTTAAGTTATTTTGATTTGTTAAAAAATATGGTAG BBBBB#<>> Writing bisulfite mapping results to EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2107:18595:54334_1:N:0:CTTGTA Scaffold_16 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2111:5981:74801_1:N:0:CTTGTA Scaffold_16 3 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:2:1316:10202:11032_1:N:0:CTTGTA Scaffold_16 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:1314:12592:63283_1:N:0:CTTGTA Scaffold_15 3 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2213:8607:54584_1:N:0:CTTGTA Scaffold_09 2 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2312:8356:27499_1:N:0:CTTGTA Scaffold_15 3 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:2:2312:6036:58634_1:N:0:CTTGTA Scaffold_15 3 27996279 reads; of these: 27996279 (100.00%) were paired; of these: 19276145 (68.85%) aligned concordantly 0 times 3764638 (13.45%) aligned concordantly exactly 1 time 4955496 (17.70%) aligned concordantly >1 times 31.15% overall alignment rate 27996279 reads; of these: 27996279 (100.00%) were paired; of these: 19163557 (68.45%) aligned concordantly 0 times 3776883 (13.49%) aligned concordantly exactly 1 time 5055839 (18.06%) aligned concordantly >1 times 31.55% overall alignment rate Processed 27996279 sequences in total Successfully deleted the temporary files EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 27996279 Number of paired-end alignments with a unique best hit: 10233767 Mapping efficiency: 36.6% Sequence pairs with no alignments under any condition: 15243065 Sequence pairs did not map uniquely: 2519447 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: 5017772 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5215988 ((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: 295230497 Total methylated C's in CpG context: 10743620 Total methylated C's in CHG context: 1476561 Total methylated C's in CHH context: 3272606 Total methylated C's in Unknown context: 54419 Total unmethylated C's in CpG context: 31907626 Total unmethylated C's in CHG context: 62815831 Total unmethylated C's in CHH context: 185014253 Total unmethylated C's in Unknown context: 638215 C methylated in CpG context: 25.2% C methylated in CHG context: 2.3% C methylated in CHH context: 1.7% C methylated in unknown context (CN or CHN): 7.9% Bismark completed in 0d 1h 24m 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 Scaffold_09 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: 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 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 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 24m 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 Scaffold_16 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:1103:17389:25945_1:N:0:CGATGT Scaffold_02 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 Scaffold_16 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 Scaffold_08 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 Scaffold_09 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:3:2109:14625:56631_1:N:0:CGATGT Scaffold_08 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 Scaffold_16 2 Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far 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 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 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 1h 55m 50s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 Scaffold_16 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 30m 24s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 1h 48m 39s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 Scaffold_09 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 Scaffold_08 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: 2068914820689148 ( reads; of these: 20689148 (100.00%) were paired; of these: 100.0013516815% () were paired; of these:65.33 % ) aligned concordantly 0 times13581727 ( 65.653053788% () aligned concordantly 0 times14.76 % ) aligned concordantly exactly 1 time3064795 ( 14.814118545% () aligned concordantly exactly 1 time19.91 % ) aligned concordantly >1 times4042626 (34.6719.54%% overall alignment rate) aligned concordantly >1 times 34.35% 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 9m 10s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 36m 14s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 Scaffold_09 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 Scaffold_16 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 Scaffold_16 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 Scaffold_16 2 Processed 22000000 sequence pairs so far 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 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 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 22m 9s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 Scaffold_16 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 11m 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 (100.00%) were paired; of these: 17323811 (64.71%) aligned concordantly 0 times 3958282 (14.79%) aligned concordantly exactly 1 time 5488376 (20.50%) aligned concordantly >1 times 35.29% overall alignment rate 26770469 reads; of these: 26770469 (100.00%) were paired; of these: 17401826 (65.00%) aligned concordantly 0 times 3983428 (14.88%) aligned concordantly exactly 1 time 5385215 (20.12%) aligned concordantly >1 times 35.00% 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 30m 1s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 510472127459153 ( reads; of these:18.59 % ) aligned concordantly >1 times27459153 (34.05% overall alignment rate 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 37m 12s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 0h 52m 13s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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/v01/ 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 Scaffold_09 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: 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 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 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 23m 24s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-205_S26_L004_R1_001_val_1.fq.gz to EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-205_S26_L004_R1_001_val_1.fq.gz (16541499 sequences in total) Writing a G -> A converted version of the input file EPI-205_S26_L004_R2_001_val_2.fq.gz to EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-205_S26_L004_R2_001_val_2.fq.gz (16541499 sequences in total) Input files are EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_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/v01/ 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-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_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:4:2315:1391:2218_1:N:0:ATCACG/1 99 Scaffold_03_CT_converted 56130216 1 45M = 56130216 -45 GATGTAGGTTGTGGTTGATGGAGAAATATTGGAAGTAGTATTTGT BBBBB/FFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2207:16029:91165_1:N:0:ATCACG Scaffold_16 2 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:4:2213:13737:21109_1:N:0:ATCACG Scaffold_16 2 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:4:1211:7255:87113_1:N:0:ATCACG Scaffold_16 2 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 16541499 reads; of these: 16541499 (100.00%) were paired; of these: 10794891 (1654149965.26 reads; of these:%) aligned concordantly 0 times 235135716541499 ( (14.21%) aligned concordantly exactly 1 time 100.00 %3395251) were paired; of these: ( 20.53 %10853410) aligned concordantly >1 times ( 65.6134.74%%) aligned concordantly 0 times overall alignment rate 2354083 (14.23%) aligned concordantly exactly 1 time 3334006 (20.16%) aligned concordantly >1 times 34.39% overall alignment rate Processed 16541499 sequences in total Successfully deleted the temporary files EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 16541499 Number of paired-end alignments with a unique best hit: 6323593 Mapping efficiency: 38.2% Sequence pairs with no alignments under any condition: 8364655 Sequence pairs did not map uniquely: 1853251 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3111821 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3211769 ((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: 172098082 Total methylated C's in CpG context: 7352466 Total methylated C's in CHG context: 973752 Total methylated C's in CHH context: 2227658 Total methylated C's in Unknown context: 41273 Total unmethylated C's in CpG context: 18563469 Total unmethylated C's in CHG context: 36797171 Total unmethylated C's in CHH context: 106183566 Total unmethylated C's in Unknown context: 362805 C methylated in CpG context: 28.4% C methylated in CHG context: 2.6% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 10.2% Bismark completed in 0d 0h 51m 19s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-206_S27_L004_R1_001_val_1.fq.gz to EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-206_S27_L004_R1_001_val_1.fq.gz (20931018 sequences in total) Writing a G -> A converted version of the input file EPI-206_S27_L004_R2_001_val_2.fq.gz to EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-206_S27_L004_R2_001_val_2.fq.gz (20931018 sequences in total) Input files are EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_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/v01/ 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-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_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:4:2315:1645:2233_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 TTATATGAGGTGGTGGTTATATTTTGATTTAATTTGAGGTTTTTTTTATTAATATGATTGG BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2103:6353:16906_1:N:0:CGATGT Scaffold_16 1 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:4:1211:14006:58140_1:N:0:CGATGT Scaffold_16 1 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 20931018 reads; of these: 20931018 (100.00%) were paired; of these: 13310092 (63.59%) aligned concordantly 0 times 3167100 (15.13%) aligned concordantly exactly 1 time 4453826 (21.28%) aligned concordantly >1 times 36.41% overall alignment rate 20931018 reads; of these: 20931018 (100.00%) were paired; of these: 13187170 (63.00%) aligned concordantly 0 times 3187504 (15.23%) aligned concordantly exactly 1 time 4556344 (21.77%) aligned concordantly >1 times 37.00% overall alignment rate Processed 20931018 sequences in total Successfully deleted the temporary files EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 20931018 Number of paired-end alignments with a unique best hit: 8694089 Mapping efficiency: 41.5% Sequence pairs with no alignments under any condition: 9860951 Sequence pairs did not map uniquely: 2375978 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: 4266342 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4427745 ((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: 247081316 Total methylated C's in CpG context: 10213182 Total methylated C's in CHG context: 1350781 Total methylated C's in CHH context: 3265902 Total methylated C's in Unknown context: 56380 Total unmethylated C's in CpG context: 26443083 Total unmethylated C's in CHG context: 53493463 Total unmethylated C's in CHH context: 152314905 Total unmethylated C's in Unknown context: 526689 C methylated in CpG context: 27.9% C methylated in CHG context: 2.5% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 9.7% Bismark completed in 0d 1h 11m 37s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-208_S28_L004_R1_001_val_1.fq.gz to EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-208_S28_L004_R1_001_val_1.fq.gz (29146503 sequences in total) Writing a G -> A converted version of the input file EPI-208_S28_L004_R2_001_val_2.fq.gz to EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-208_S28_L004_R2_001_val_2.fq.gz (29146503 sequences in total) Input files are EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_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/v01/ 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-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_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:4:2315:1156:2191_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 ATGTTTTATTTTTTAGANATAATAGGTTAANNNTNTNNNNTGTAGTATTTAGNGGTTNGNNNGGAAGAGTATATGTTTGAATTTTAGTTATTTAGGTATTT BBBBBFF>> Writing bisulfite mapping results to EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_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:4:2305:8854:87586_1:N:0:TTAGGC Scaffold_08 61151067 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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1313:10573:73734_1:N:0:TTAGGC Scaffold_10 1 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:4:1201:5663:17431_1:N:0:TTAGGC Scaffold_09 2 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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1112:15304:52396_1:N:0:TTAGGC Scaffold_10 1 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 29146503 reads; of these: 29146503 (100.00%) were paired; of these: 18935303 (64.97%) aligned concordantly 0 times 4124381 (14.15%) aligned concordantly exactly 1 time 6086819 (20.88%) aligned concordantly >1 times 35.03% overall alignment rate 29146503 reads; of these: 29146503 (100.00%) were paired; of these: 18852155 (64.68%) aligned concordantly 0 times 4094007 (14.05%) aligned concordantly exactly 1 time 6200341 (21.27%) aligned concordantly >1 times 35.32% overall alignment rate Processed 29146503 sequences in total Successfully deleted the temporary files EPI-208_S28_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-208_S28_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29146503 Number of paired-end alignments with a unique best hit: 11240949 Mapping efficiency: 38.6% Sequence pairs with no alignments under any condition: 14550345 Sequence pairs did not map uniquely: 3355209 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: 5552476 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5688469 ((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: 311618922 Total methylated C's in CpG context: 11403965 Total methylated C's in CHG context: 1731400 Total methylated C's in CHH context: 3248557 Total methylated C's in Unknown context: 54196 Total unmethylated C's in CpG context: 33743386 Total unmethylated C's in CHG context: 67489106 Total unmethylated C's in CHH context: 194002508 Total unmethylated C's in Unknown context: 680321 C methylated in CpG context: 25.3% C methylated in CHG context: 2.5% C methylated in CHH context: 1.6% C methylated in unknown context (CN or CHN): 7.4% Bismark completed in 0d 1h 31m 27s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-209_S29_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-209_S29_L004_R1_001_val_1.fq.gz to EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-209_S29_L004_R1_001_val_1.fq.gz (29638248 sequences in total) Writing a G -> A converted version of the input file EPI-209_S29_L004_R2_001_val_2.fq.gz to EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-209_S29_L004_R2_001_val_2.fq.gz (29638248 sequences in total) Input files are EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_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/v01/ 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-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_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:4:2315:1317:2220_1:N:0:TGACCA/1 99 Scaffold_10_CT_converted 32311949 42 87M = 32311949 -87 TAAAGGTATTGGATTAGTTATTGTTGTATGAGTAAAGAATGTATATAATAAATATGATTTTAAATAGTTTTAGTTGATATATTAGGT BB>> Writing bisulfite mapping results to EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2207:11600:61311_1:N:0:TGACCA Scaffold_09 1 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2312:14878:45622_1:N:0:TGACCA Scaffold_09 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1209:21220:77577_1:N:0:TGACCA Scaffold_09 1 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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1102:10195:40194_1:N:0:TGACCA Scaffold_16 3 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1114:18083:94909_1:N:0:TGACCA Scaffold_09 2 Processed 29000000 sequence pairs so far 29638248 reads; of these: 29638248 (100.00%) were paired; of these: 19011220 (64.14%) aligned concordantly 0 times 4547140 (15.34%) aligned concordantly exactly 1 time 6079888 (20.51%) aligned concordantly >1 times 35.86% overall alignment rate 29638248 reads; of these: 29638248 (100.00%) were paired; of these: 19174450 (64.69%) aligned concordantly 0 times 4514082 (15.23%) aligned concordantly exactly 1 time 5949716 (20.07%) aligned concordantly >1 times 35.31% overall alignment rate Processed 29638248 sequences in total Successfully deleted the temporary files EPI-209_S29_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-209_S29_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29638248 Number of paired-end alignments with a unique best hit: 12390019 Mapping efficiency: 41.8% Sequence pairs with no alignments under any condition: 14317340 Sequence pairs did not map uniquely: 2930889 Sequence pairs which were discarded because genomic sequence could not be extracted: 5 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6084990 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6305024 ((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: 367398872 Total methylated C's in CpG context: 15426958 Total methylated C's in CHG context: 1845531 Total methylated C's in CHH context: 4197293 Total methylated C's in Unknown context: 75507 Total unmethylated C's in CpG context: 38606002 Total unmethylated C's in CHG context: 78585196 Total unmethylated C's in CHH context: 228737892 Total unmethylated C's in Unknown context: 791989 C methylated in CpG context: 28.6% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 8.7% Bismark completed in 0d 1h 42m 27s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-214_S30_L004_R1_001_val_1.fq.gz to EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-214_S30_L004_R1_001_val_1.fq.gz (28660043 sequences in total) Writing a G -> A converted version of the input file EPI-214_S30_L004_R2_001_val_2.fq.gz to EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-214_S30_L004_R2_001_val_2.fq.gz (28660043 sequences in total) Input files are EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_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/v01/ 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-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_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:4:2315:1228:2242_1:N:0:ACAGTG/1 99 Scaffold_18_CT_converted 25379951 1 41M = 25379951 -41 TAAGATGTATTTTTATAGTATAATGAAGTATATTTATTTTT BBBBBFFFFFFFFFFFFFFFFBBFFBFFFFFFFFFBFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:41 YS:i:0 YT:Z:CP D00743:144:CAAWNANXX:4:2315:1228:2242_2:N:0:ACAGTG/2 147 Scaffold_18_CT_converted 25379951 1 41M = 25379951 -41 TAAGATGTATTTTTATAGTATAATGAAGTATATTTATTTTT FFFFFFFFFFFFFFFFFFBFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2307:21282:95127_1:N:0:ACAGTG Scaffold_09 2 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:4:2302:8005:16451_1:N:0:ACAGTG Scaffold_09 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 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2204:7409:50593_1:N:0:ACAGTG Scaffold_09 1 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2112:4091:16831_1:N:0:ACAGTG Scaffold_09 1 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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1109:11354:68408_1:N:0:ACAGTG Scaffold_09 1 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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1106:11751:57911_1:N:0:ACAGTG Scaffold_09 1 28660043 reads; of these: 28660043 (100.00%) were paired; of these: 18987602 (66.25%) aligned concordantly 0 times 4195301 (14.64%) aligned concordantly exactly 1 time 5477140 (19.11%) aligned concordantly >1 times 33.75% overall alignment rate 28660043 reads; of these: 28660043 (100.00%) were paired; of these: 19060313 (66.50%) aligned concordantly 0 times 4198728 (14.65%) aligned concordantly exactly 1 time 5401002 (18.85%) aligned concordantly >1 times 33.50% overall alignment rate Processed 28660043 sequences in total Successfully deleted the temporary files EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28660043 Number of paired-end alignments with a unique best hit: 11468074 Mapping efficiency: 40.0% Sequence pairs with no alignments under any condition: 14622941 Sequence pairs did not map uniquely: 2569028 Sequence pairs which were discarded because genomic sequence could not be extracted: 6 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5665121 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5802947 ((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: 344103876 Total methylated C's in CpG context: 13048066 Total methylated C's in CHG context: 1676923 Total methylated C's in CHH context: 4069143 Total methylated C's in Unknown context: 63794 Total unmethylated C's in CpG context: 35864648 Total unmethylated C's in CHG context: 72383593 Total unmethylated C's in CHH context: 217061503 Total unmethylated C's in Unknown context: 751976 C methylated in CpG context: 26.7% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 7.8% Bismark completed in 0d 1h 36m 58s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-215_S31_L004_R1_001_val_1.fq.gz to EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-215_S31_L004_R1_001_val_1.fq.gz (21150005 sequences in total) Writing a G -> A converted version of the input file EPI-215_S31_L004_R2_001_val_2.fq.gz to EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-215_S31_L004_R2_001_val_2.fq.gz (21150005 sequences in total) Input files are EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_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/v01/ 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-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_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:4:2315:1539:2240_1:N:0:GCCAAT/1 99 Scaffold_13_CT_converted 10986848 1 101M = 10986886 137 ATGGTAGTAGAGTGTTGGATTAATATTGGGGTTTGTATGTTTGAGTGTATGGTTTAGTAGTAGAGTGTTGGATTAATATTGGGGGTTGTATGTTTGAGTGT BBBBBFF>> Writing bisulfite mapping results to EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_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 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1305:3900:27082_1:N:0:GCCAAT Scaffold_09 1 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 21150005 reads; of these: 21150005 (100.00%) were paired; of these: 13428551 (63.49%) aligned concordantly 0 times 3294139 (15.58%) aligned concordantly exactly 1 time 4427315 (20.93%) aligned concordantly >1 times 36.51% overall alignment rate 21150005 reads; of these: 21150005 (100.00%) were paired; of these: 13330719 (63.03%) aligned concordantly 0 times 3311858 (15.66%) aligned concordantly exactly 1 time 4507428 (21.31%) aligned concordantly >1 times 36.97% overall alignment rate Processed 21150005 sequences in total Successfully deleted the temporary files EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 21150005 Number of paired-end alignments with a unique best hit: 8898558 Mapping efficiency: 42.1% Sequence pairs with no alignments under any condition: 9932657 Sequence pairs did not map uniquely: 2318790 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: 4386310 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4512247 ((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: 255324646 Total methylated C's in CpG context: 11359862 Total methylated C's in CHG context: 1449582 Total methylated C's in CHH context: 3434042 Total methylated C's in Unknown context: 63236 Total unmethylated C's in CpG context: 25363136 Total unmethylated C's in CHG context: 54116553 Total unmethylated C's in CHH context: 159601471 Total unmethylated C's in Unknown context: 546779 C methylated in CpG context: 30.9% C methylated in CHG context: 2.6% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 10.4% Bismark completed in 0d 1h 11m 16s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-220_S32_L004_R1_001_val_1.fq.gz to EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-220_S32_L004_R1_001_val_1.fq.gz (15670592 sequences in total) Writing a G -> A converted version of the input file EPI-220_S32_L004_R2_001_val_2.fq.gz to EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-220_S32_L004_R2_001_val_2.fq.gz (15670592 sequences in total) Input files are EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_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/v01/ 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-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_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:4:2315:1490:2220_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TTTTTTGGTTGTTGTATGGTGTTGTTGTATAGTGTTGTGGTGTTGTTGTATGGTGTTGGTATATGGTGTTGTGGTGTTATGTATGGTGTTGTGGTGTTGGT BBBBBFFFFFFBFFFFFFF/BFFFFFBF/FFFFFFFFFFFBF>> Writing bisulfite mapping results to EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_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:4:2116:14308:81928_1:N:0:CAGATC Scaffold_16 2 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 15670592 reads; of these: 15670592 (100.00%) were paired; of these: 10271084 (65.54%) aligned concordantly 0 times 2353216 (15.02%) aligned concordantly exactly 1 time 3046292 (19.44%) aligned concordantly >1 times 34.46% overall alignment rate 15670592 reads; of these: 15670592 (100.00%) were paired; of these: 10197163 (65.07%) aligned concordantly 0 times 2371554 (15.13%) aligned concordantly exactly 1 time 3101875 (19.79%) aligned concordantly >1 times 34.93% overall alignment rate Processed 15670592 sequences in total Successfully deleted the temporary files EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 15670592 Number of paired-end alignments with a unique best hit: 6443741 Mapping efficiency: 41.1% Sequence pairs with no alignments under any condition: 7744109 Sequence pairs did not map uniquely: 1482742 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: 3171588 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3272152 ((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: 192776371 Total methylated C's in CpG context: 7792143 Total methylated C's in CHG context: 1027385 Total methylated C's in CHH context: 3406922 Total methylated C's in Unknown context: 57729 Total unmethylated C's in CpG context: 19534468 Total unmethylated C's in CHG context: 40565305 Total unmethylated C's in CHH context: 120450148 Total unmethylated C's in Unknown context: 422486 C methylated in CpG context: 28.5% C methylated in CHG context: 2.5% C methylated in CHH context: 2.8% C methylated in unknown context (CN or CHN): 12.0% Bismark completed in 0d 0h 53m 37s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-221_S33_L004_R1_001_val_1.fq.gz to EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-221_S33_L004_R1_001_val_1.fq.gz (16300374 sequences in total) Writing a G -> A converted version of the input file EPI-221_S33_L004_R2_001_val_2.fq.gz to EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-221_S33_L004_R2_001_val_2.fq.gz (16300374 sequences in total) Input files are EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_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/v01/ 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-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_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:4:2315:1412:2190_1:N:0:ACTTGA/1 99 Scaffold_13_CT_converted 41856358 2 98M = 41856393 133 ATTTTNTGTTTTATGTTTTATTTTTATTTTAGTGTTTGAAAAAATTTTGGAGAAAGGTAGATATTTTTTAGTGGTTGTAAAAAATATAAGTTGGATTG BBBBB#BBBBFFFFFFFFFFFFFFFFFFFFFBF7FFFFF>> Writing bisulfite mapping results to EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2211:4716:98965_1:N:0:ACTTGA Scaffold_09 2 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2103:13364:91695_1:N:0:ACTTGA Scaffold_16 2 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far 16300374 reads; of these: 16300374 (100.00%) were paired; of these: 10304625 (63.22%) aligned concordantly 0 times 2553714 (15.67%) aligned concordantly exactly 1 time 3442035 (21.12%) aligned concordantly >1 times 36.78% overall alignment rate 16300374 reads; of these: 16300374 (100.00%) were paired; of these: 10247311 (62.87%) aligned concordantly 0 times 2557704 (15.69%) aligned concordantly exactly 1 time 3495359 (21.44%) aligned concordantly >1 times 37.13% overall alignment rate Processed 16300374 sequences in total Successfully deleted the temporary files EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 16300374 Number of paired-end alignments with a unique best hit: 6871477 Mapping efficiency: 42.2% Sequence pairs with no alignments under any condition: 7612342 Sequence pairs did not map uniquely: 1816555 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: 3394540 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3476935 ((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: 195629573 Total methylated C's in CpG context: 8208009 Total methylated C's in CHG context: 1115053 Total methylated C's in CHH context: 3356022 Total methylated C's in Unknown context: 59602 Total unmethylated C's in CpG context: 19626346 Total unmethylated C's in CHG context: 41123332 Total unmethylated C's in CHH context: 122200811 Total unmethylated C's in Unknown context: 418497 C methylated in CpG context: 29.5% C methylated in CHG context: 2.6% C methylated in CHH context: 2.7% C methylated in unknown context (CN or CHN): 12.5% Bismark completed in 0d 0h 55m 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-226_S34_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-226_S34_L004_R1_001_val_1.fq.gz to EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-226_S34_L004_R1_001_val_1.fq.gz (11133150 sequences in total) Writing a G -> A converted version of the input file EPI-226_S34_L004_R2_001_val_2.fq.gz to EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-226_S34_L004_R2_001_val_2.fq.gz (11133150 sequences in total) Input files are EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_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/v01/ 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-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_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:4:2315:1168:2235_1:N:0:GATCAG/1 99 Scaffold_09_CT_converted 21134968 1 84M = 21134968 -84 TTATATTATATTTTATANTGTGTAAAGTTGTNGTTAAGTGATTTATATTTGTNGTATTTTNNTTGTTATTGTTTATATAGTGGG BBBBBFFFFFFFFFFBF#BB>> Writing bisulfite mapping results to EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_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 11133150 reads; of these: 11133150 (100.00%) were paired; of these: 7275943 (65.35%) aligned concordantly 0 times 1704164 (15.31%) aligned concordantly exactly 1 time 2153043 (19.34%) aligned concordantly >1 times 34.65% overall alignment rate 11133150 reads; of these: 11133150 (100.00%) were paired; of these: 7326692 (65.81%) aligned concordantly 0 times 1687118 (15.15%) aligned concordantly exactly 1 time 2119340 (19.04%) aligned concordantly >1 times 34.19% overall alignment rate Processed 11133150 sequences in total Successfully deleted the temporary files EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 11133150 Number of paired-end alignments with a unique best hit: 4644692 Mapping efficiency: 41.7% Sequence pairs with no alignments under any condition: 5510557 Sequence pairs did not map uniquely: 977901 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: 2290844 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2353848 ((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: 142579752 Total methylated C's in CpG context: 6040169 Total methylated C's in CHG context: 756511 Total methylated C's in CHH context: 2622283 Total methylated C's in Unknown context: 41120 Total unmethylated C's in CpG context: 13986909 Total unmethylated C's in CHG context: 29876966 Total unmethylated C's in CHH context: 89296914 Total unmethylated C's in Unknown context: 314802 C methylated in CpG context: 30.2% C methylated in CHG context: 2.5% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 11.6% Bismark completed in 0d 0h 38m 30s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-227_S35_L004_R1_001_val_1.fq.gz to EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-227_S35_L004_R1_001_val_1.fq.gz (13531234 sequences in total) Writing a G -> A converted version of the input file EPI-227_S35_L004_R2_001_val_2.fq.gz to EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-227_S35_L004_R2_001_val_2.fq.gz (13531234 sequences in total) Input files are EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_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/v01/ 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-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_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:4:2315:1203:2205_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 TTTGTTTTTTTTTATATATAAATTATTAATTAAATAATTTAATTTTGTAAAANTTGTAAAANTATATAAATATTTATGTATTATTTTAATATTTTATAGTT BBBBB>> Writing bisulfite mapping results to EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_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:4:1114:15289:101085_1:N:0:TAGCTT Scaffold_09 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1106:15612:24235_1:N:0:TAGCTT Scaffold_09 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1106:5390:26206_1:N:0:TAGCTT Scaffold_09 1 13531234 reads; of these: 13531234 (100.00%) were paired; of these: 8564398 (63.29%) aligned concordantly 0 times 2130788 (15.75%) aligned concordantly exactly 1 time 2836048 (20.96%) aligned concordantly >1 times 36.71% overall alignment rate 13531234 reads; of these: 13531234 (100.00%) were paired; of these: 8607387 (63.61%) aligned concordantly 0 times 2127294 (15.72%) aligned concordantly exactly 1 time 2796553 (20.67%) aligned concordantly >1 times 36.39% overall alignment rate Processed 13531234 sequences in total Successfully deleted the temporary files EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 13531234 Number of paired-end alignments with a unique best hit: 5777321 Mapping efficiency: 42.7% Sequence pairs with no alignments under any condition: 6365101 Sequence pairs did not map uniquely: 1388812 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2853863 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2923455 ((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: 170387967 Total methylated C's in CpG context: 7151061 Total methylated C's in CHG context: 914187 Total methylated C's in CHH context: 3215757 Total methylated C's in Unknown context: 47223 Total unmethylated C's in CpG context: 16695256 Total unmethylated C's in CHG context: 35577795 Total unmethylated C's in CHH context: 106833911 Total unmethylated C's in Unknown context: 363445 C methylated in CpG context: 30.0% C methylated in CHG context: 2.5% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 11.5% Bismark completed in 0d 0h 47m 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-229_S36_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-229_S36_L004_R1_001_val_1.fq.gz to EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-229_S36_L004_R1_001_val_1.fq.gz (19891722 sequences in total) Writing a G -> A converted version of the input file EPI-229_S36_L004_R2_001_val_2.fq.gz to EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-229_S36_L004_R2_001_val_2.fq.gz (19891722 sequences in total) Input files are EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_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/v01/ 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-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_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:4:2315:1979:2198_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 TGTATAGTATAGTTTAGTGTTGTGGTTAGTTTTAATATAGAAATATTAATTTTAATTTAATGTGATGTATTTAGAAAGTTTTAGAAAGTTTGTGGTAG B/BBBFFFF>> Writing bisulfite mapping results to EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2313:17038:73178_1:N:0:GGCTAC Scaffold_16 1 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 19891722 reads; of these: 19891722 (100.00%19891722) were paired; of these: reads; of these: 1311908819891722 ( (65.95%) aligned concordantly 0 times 100.002905732% () were paired; of these:14.61 % ) aligned concordantly exactly 1 time13000744 ( 65.363866902% () aligned concordantly 0 times19.44 % ) aligned concordantly >1 times2936830 (34.0514.76%% overall alignment rate) aligned concordantly exactly 1 time 3954148 (19.88%) aligned concordantly >1 times 34.64% overall alignment rate Processed 19891722 sequences in total Successfully deleted the temporary files EPI-229_S36_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-229_S36_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 19891722 Number of paired-end alignments with a unique best hit: 8020238 Mapping efficiency: 40.3% Sequence pairs with no alignments under any condition: 9946231 Sequence pairs did not map uniquely: 1925253 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: 3928266 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4091971 ((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: 234928287 Total methylated C's in CpG context: 9402130 Total methylated C's in CHG context: 1206978 Total methylated C's in CHH context: 3281401 Total methylated C's in Unknown context: 62587 Total unmethylated C's in CpG context: 24903264 Total unmethylated C's in CHG context: 50373954 Total unmethylated C's in CHH context: 145760560 Total unmethylated C's in Unknown context: 512946 C methylated in CpG context: 27.4% C methylated in CHG context: 2.3% C methylated in CHH context: 2.2% C methylated in unknown context (CN or CHN): 10.9% Bismark completed in 0d 1h 5m 9s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_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/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (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-230_S37_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-230_S37_L004_R1_001_val_1.fq.gz to EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-230_S37_L004_R1_001_val_1.fq.gz (29439432 sequences in total) Writing a G -> A converted version of the input file EPI-230_S37_L004_R2_001_val_2.fq.gz to EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-230_S37_L004_R2_001_val_2.fq.gz (29439432 sequences in total) Input files are EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_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/v01/ 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-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_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:4:2315:1161:2210_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 ATTTTGTATATGGTATANATTTAGTTTGATTNNTNANATNGGTGAATGATGTNGTATATNNNTTGTTTGATTGGTAAAATGGGTGAATGATGTTATATATG BBBBBFFFFFFFFFFFF#B<>> Writing bisulfite mapping results to EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1309:15438:42412_1:N:0:CTTGTA Scaffold_16 2 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1214:8602:31140_1:N:0:CTTGTA Scaffold_16 2 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1104:14877:71207_1:N:0:CTTGTA Scaffold_15 3 Processed 29000000 sequence pairs so far 29439432 reads; of these: 29439432 (100.00%) were paired; of these: 19725091 (67.00%) aligned concordantly 0 times 4124627 (14.01%) aligned concordantly exactly 1 time 5589714 (18.99%) aligned concordantly >1 times 33.00% overall alignment rate 29439432 reads; of these: 29439432 (100.00%) were paired; of these: 19816927 (67.31%) aligned concordantly 0 times 4140780 (14.07%) aligned concordantly exactly 1 time 5481725 (18.62%) aligned concordantly >1 times 32.69% overall alignment rate Processed 29439432 sequences in total Successfully deleted the temporary files EPI-230_S37_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-230_S37_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29439432 Number of paired-end alignments with a unique best hit: 11206080 Mapping efficiency: 38.1% Sequence pairs with no alignments under any condition: 15456327 Sequence pairs did not map uniquely: 2777025 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5519967 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5686110 ((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: 319285007 Total methylated C's in CpG context: 13011809 Total methylated C's in CHG context: 1476854 Total methylated C's in CHH context: 3593317 Total methylated C's in Unknown context: 73261 Total unmethylated C's in CpG context: 33278910 Total unmethylated C's in CHG context: 67397808 Total unmethylated C's in CHH context: 200526309 Total unmethylated C's in Unknown context: 692785 C methylated in CpG context: 28.1% C methylated in CHG context: 2.1% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 9.6% Bismark completed in 0d 1h 31m 57s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-41_S38_L005_R1_001_val_1.fq.gz to EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-41_S38_L005_R1_001_val_1.fq.gz (25055317 sequences in total) Writing a G -> A converted version of the input file EPI-41_S38_L005_R2_001_val_2.fq.gz to EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-41_S38_L005_R2_001_val_2.fq.gz (25055317 sequences in total) Input files are EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1186:2238_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 GTAGTNTTGGTTGGAATATATATTGTATTGTTATTTGTATTTGGTATATAAGNGGTATNGTNGTTGGTGTTTGGTGTGTAAGTAGTATTGTTGTTGGAGTT BBBBB#>> Writing bisulfite mapping results to EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:5:1203:12890:67154_1:N:0:ATCACG Scaffold_16 2 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:5:2309:19429:51893_1:N:0:ATCACG Scaffold_16 2 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far 25055317 reads; of these: 25055317 (100.00%) were paired; of these: 16269403 (64.93%) aligned concordantly 0 times 3783069 (15.10%) aligned concordantly exactly 1 time 5002845 (19.97%) aligned concordantly >1 times 35.07% overall alignment rate 25055317 reads; of these: 25055317 (100.00%) were paired; of these: 16350090 (65.26%) aligned concordantly 0 times 3786709 (15.11%) aligned concordantly exactly 1 time 4918518 (19.63%) aligned concordantly >1 times 34.74% overall alignment rate Processed 25055317 sequences in total Successfully deleted the temporary files EPI-41_S38_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-41_S38_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 25055317 Number of paired-end alignments with a unique best hit: 10110534 Mapping efficiency: 40.4% Sequence pairs with no alignments under any condition: 12402840 Sequence pairs did not map uniquely: 2541943 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4993663 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5116869 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 290510503 Total methylated C's in CpG context: 12940226 Total methylated C's in CHG context: 1543391 Total methylated C's in CHH context: 4910085 Total methylated C's in Unknown context: 96039 Total unmethylated C's in CpG context: 28119492 Total unmethylated C's in CHG context: 60698341 Total unmethylated C's in CHH context: 182298968 Total unmethylated C's in Unknown context: 604385 C methylated in CpG context: 31.5% C methylated in CHG context: 2.5% C methylated in CHH context: 2.6% C methylated in unknown context (CN or CHN): 13.7% Bismark completed in 0d 1h 21m 45s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-42_S39_L005_R1_001_val_1.fq.gz to EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-42_S39_L005_R1_001_val_1.fq.gz (29623269 sequences in total) Writing a G -> A converted version of the input file EPI-42_S39_L005_R2_001_val_2.fq.gz to EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-42_S39_L005_R2_001_val_2.fq.gz (29623269 sequences in total) Input files are EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1597:2224_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 AGGTANTATGATGTGATGATGGGGTATGATGTGAAGATGGG BBBBB#BBFFFFFFFFFFFFFFFFBFFBFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:5:1107:1597:2224_2:N:0:CGATGT/2 141 * 0 0 * * 0 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNCCT ####################################<#<>> Writing bisulfite mapping results to EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 29623269 reads; of these: 29623269 (100.00%) were paired; of these: 18241307 (61.58%) aligned concordantly 0 times 4905564 (16.56%) aligned concordantly exactly 1 time 6476398 (21.86%) aligned concordantly >1 times 38.42% overall alignment rate 29623269 reads; of these: 29623269 (100.00%) were paired; of these: 18159622 (61.30%) aligned concordantly 0 times 4916719 (16.60%) aligned concordantly exactly 1 time 6546928 (22.10%) aligned concordantly >1 times 38.70% overall alignment rate Processed 29623269 sequences in total Successfully deleted the temporary files EPI-42_S39_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-42_S39_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29623269 Number of paired-end alignments with a unique best hit: 13173399 Mapping efficiency: 44.5% Sequence pairs with no alignments under any condition: 13088150 Sequence pairs did not map uniquely: 3361720 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6518218 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6655181 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 371864315 Total methylated C's in CpG context: 17401813 Total methylated C's in CHG context: 2029825 Total methylated C's in CHH context: 4531660 Total methylated C's in Unknown context: 68790 Total unmethylated C's in CpG context: 35533244 Total unmethylated C's in CHG context: 78200824 Total unmethylated C's in CHH context: 234166949 Total unmethylated C's in Unknown context: 781521 C methylated in CpG context: 32.9% C methylated in CHG context: 2.5% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 8.1% Bismark completed in 0d 1h 44m 30s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-43_S40_L005_R1_001_val_1.fq.gz to EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-43_S40_L005_R1_001_val_1.fq.gz (22573555 sequences in total) Writing a G -> A converted version of the input file EPI-43_S40_L005_R2_001_val_2.fq.gz to EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-43_S40_L005_R2_001_val_2.fq.gz (22573555 sequences in total) Input files are EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1481:2240_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 TTTTAATATTAATATATTAAAATATAAAATTTTTATAATTATAATATATATAAATATTATAATATTAATATATTAATATAAAAATTTTATATAATTATAAT BBBBBFF>> Writing bisulfite mapping results to EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far 22573555 reads; of these: 22573555 (100.00%) were paired; of these: 13873582 (61.46%) aligned concordantly 0 times 3802013 (16.84%) aligned concordantly exactly 1 time 4897960 (21.70%) aligned concordantly >1 times 38.54% overall alignment rate 22573555 reads; of these: 22573555 (100.00%) were paired; of these: 13942903 (61.77%) aligned concordantly 0 times 3795765 (16.82%) aligned concordantly exactly 1 time 4834887 (21.42%) aligned concordantly >1 times 38.23% overall alignment rate Processed 22573555 sequences in total Successfully deleted the temporary files EPI-43_S40_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-43_S40_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 22573555 Number of paired-end alignments with a unique best hit: 10112774 Mapping efficiency: 44.8% Sequence pairs with no alignments under any condition: 10003930 Sequence pairs did not map uniquely: 2456851 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5003413 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5109361 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 291124282 Total methylated C's in CpG context: 12587981 Total methylated C's in CHG context: 1494744 Total methylated C's in CHH context: 5077384 Total methylated C's in Unknown context: 67963 Total unmethylated C's in CpG context: 28303550 Total unmethylated C's in CHG context: 60291324 Total unmethylated C's in CHH context: 183369299 Total unmethylated C's in Unknown context: 592883 C methylated in CpG context: 30.8% C methylated in CHG context: 2.4% C methylated in CHH context: 2.7% C methylated in unknown context (CN or CHN): 10.3% Bismark completed in 0d 1h 19m 43s ==================== 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/v01/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)' 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/sr320/1218'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1218 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-44_S41_L005_R1_001_val_1.fq.gz to EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-44_S41_L005_R1_001_val_1.fq.gz (13762658 sequences in total) Writing a G -> A converted version of the input file EPI-44_S41_L005_R2_001_val_2.fq.gz to EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-44_S41_L005_R2_001_val_2.fq.gz (13762658 sequences in total) Input files are EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:5:1107:1348:2233_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AATTTNGGTGTATAGTTTAAGTTAGGAAAGTTTTTTTTATTAAATTGTTTTGTTATGTTTAAATAGATATTTTTTTGGTAGTAT BBBBB#/B>> Writing bisulfite mapping results to EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:5:1215:4007:34225_1:N:0:ACTTGA Scaffold_09 1 13762658 reads; of these: 13762658 (100.00%) were paired; of these: 8493354 (61.71%) aligned concordantly 0 times 2308211 (16.77%) aligned concordantly exactly 1 time 2961093 (21.52%) aligned concordantly >1 times 38.29% overall alignment rate 13762658 reads; of these: 13762658 (100.00%) were paired; of these: 8468686 (61.53%) aligned concordantly 0 times 2306213 (16.76%) aligned concordantly exactly 1 time 2987759 (21.71%) aligned concordantly >1 times 38.47% overall alignment rate Processed 13762658 sequences in total Successfully deleted the temporary files EPI-44_S41_L005_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-44_S41_L005_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 13762658 Number of paired-end alignments with a unique best hit: 6084805 Mapping efficiency: 44.2% Sequence pairs with no alignments under any condition: 6118468 Sequence pairs did not map uniquely: 1559385 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3020647 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3064157 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 170813493 Total methylated C's in CpG context: 8105964 Total methylated C's in CHG context: 922535 Total methylated C's in CHH context: 2562650 Total methylated C's in Unknown context: 43087 Total unmethylated C's in CpG context: 16050613 Total unmethylated C's in CHG context: 35418280 Total unmethylated C's in CHH context: 107753451 Total unmethylated C's in Unknown context: 349691 C methylated in CpG context: 33.6% C methylated in CHG context: 2.5% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 11.0% Bismark completed in 0d 0h 48m 36s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam: 9095591 Total number duplicated alignments removed: 1259755 (13.85%) Duplicated alignments were found at: 632529 different position(s) Total count of deduplicated leftover sequences: 7835836 (86.15% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 7835836 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 7835836 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:2212:20778:92240_1:N:0:ATCACG) and Read 2 (SL-HBW:624:CAAWVANXX:5:2208:17637:29074_1:N:0:ATCACG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam: 13633935 Total number duplicated alignments removed: 2020190 (14.82%) Duplicated alignments were found at: 1117791 different position(s) Total count of deduplicated leftover sequences: 11613745 (85.18% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 11613745 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 11613745 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:1112:11910:20560_1:N:0:CGATGT) and Read 2 (SL-HBW:624:CAAWVANXX:5:2103:4166:29334_1:N:0:CGATGT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam: 12312882 Total number duplicated alignments removed: 1846060 (14.99%) Duplicated alignments were found at: 941145 different position(s) Total count of deduplicated leftover sequences: 10466822 (85.01% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 10466822 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 10466822 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:1302:11840:79390_1:N:0:TTAGGC) and Read 2 (SL-HBW:624:CAAWVANXX:5:2112:14306:25179_1:N:0:TTAGGC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam: 11581685 Total number duplicated alignments removed: 1726942 (14.91%) Duplicated alignments were found at: 879906 different position(s) Total count of deduplicated leftover sequences: 9854743 (85.09% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 9854743 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 9854743 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:2309:4144:24028_1:N:0:TGACCA) and Read 2 (SL-HBW:624:CAAWVANXX:5:1301:5442:25828_1:N:0:TGACCA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam: 12331886 Total number duplicated alignments removed: 1918064 (15.55%) Duplicated alignments were found at: 946129 different position(s) Total count of deduplicated leftover sequences: 10413822 (84.45% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 10413822 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 10413822 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:1213:16989:56223_1:N:0:ACAGTG) and Read 2 (SL-HBW:624:CAAWVANXX:5:1301:5790:74023_1:N:0:ACAGTG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam: 11050080 Total number duplicated alignments removed: 1579974 (14.30%) Duplicated alignments were found at: 825606 different position(s) Total count of deduplicated leftover sequences: 9470106 (85.70% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 9470106 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 9470106 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:1306:18249:2701_1:N:0:GCCAAT) and Read 2 (SL-HBW:624:CAAWVANXX:5:1114:12645:7689_1:N:0:GCCAAT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam: 9986594 Total number duplicated alignments removed: 1536515 (15.39%) Duplicated alignments were found at: 782021 different position(s) Total count of deduplicated leftover sequences: 8450079 (84.61% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 8450079 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 8450079 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:1108:5881:16544_1:N:0:CAGATC) and Read 2 (SL-HBW:624:CAAWVANXX:5:1103:5704:30606_1:N:0:CAGATC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam: 11023910 Total number duplicated alignments removed: 1723786 (15.64%) Duplicated alignments were found at: 865786 different position(s) Total count of deduplicated leftover sequences: 9300124 (84.36% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 9300124 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 9300124 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:2316:6217:54235_1:N:0:ACTTGA) and Read 2 (SL-HBW:624:CAAWVANXX:5:2209:10572:22469_1:N:0:ACTTGA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam: 12720630 Total number duplicated alignments removed: 2161126 (16.99%) Duplicated alignments were found at: 1085821 different position(s) Total count of deduplicated leftover sequences: 10559504 (83.01% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 10559504 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 10559504 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:2108:5541:32073_1:N:0:GATCAG) and Read 2 (SL-HBW:624:CAAWVANXX:5:1208:19496:77087_1:N:0:GATCAG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam: 12229033 Total number duplicated alignments removed: 1939155 (15.86%) Duplicated alignments were found at: 929619 different position(s) Total count of deduplicated leftover sequences: 10289878 (84.14% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 10289878 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 10289878 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:1105:18038:76225_1:N:0:TAGCTT) and Read 2 (SL-HBW:624:CAAWVANXX:5:2315:3072:56604_1:N:0:TAGCTT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam: 9316818 Total number duplicated alignments removed: 1420739 (15.25%) Duplicated alignments were found at: 811691 different position(s) Total count of deduplicated leftover sequences: 7896079 (84.75% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 7896079 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 7896079 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:1107:15380:100924_1:N:0:GGCTAC) and Read 2 (SL-HBW:624:CAAWVANXX:5:1307:4081:96380_1:N:0:GGCTAC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam: 11191274 Total number duplicated alignments removed: 1835341 (16.40%) Duplicated alignments were found at: 997702 different position(s) Total count of deduplicated leftover sequences: 9355933 (83.60% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 9355933 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 9355933 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (SL-HBW:624:CAAWVANXX:5:1308:20849:67956_1:N:0:CTTGTA) and Read 2 (SL-HBW:624:CAAWVANXX:5:2116:2813:56256_1:N:0:CTTGTA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-151_S2_L002_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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam: 9915441 Total number duplicated alignments removed: 2705164 (27.28%) Duplicated alignments were found at: 1698251 different position(s) Total count of deduplicated leftover sequences: 7210277 (72.72% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 7210277 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 7210277 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:2202:10588:98148_1:N:0:ATCACG) and Read 2 (D00743:144:CAAWNANXX:2:1115:9962:19961_1:N:0:ATCACG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-152_S3_L002_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-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam: 11727816 Total number duplicated alignments removed: 3318046 (28.29%) Duplicated alignments were found at: 2042936 different position(s) Total count of deduplicated leftover sequences: 8409770 (71.71% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 8409770 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 8409770 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:2313:10413:17810_1:N:0:CGATGT) and Read 2 (D00743:144:CAAWNANXX:2:2103:1409:47116_1:N:0:CGATGT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-153_S4_L002_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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam: 10439071 Total number duplicated alignments removed: 3739516 (35.82%) Duplicated alignments were found at: 2094280 different position(s) Total count of deduplicated leftover sequences: 6699555 (64.18% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6699555 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6699555 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:2205:13660:31538_1:N:0:TTAAGC) and Read 2 (D00743:144:CAAWNANXX:2:2116:4283:52179_1:N:0:TTAGGA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-154_S5_L002_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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam: 9405544 Total number duplicated alignments removed: 2636021 (28.03%) Duplicated alignments were found at: 1665648 different position(s) Total count of deduplicated leftover sequences: 6769523 (71.97% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6769523 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6769523 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:2310:16530:100783_1:N:0:TGACCA) and Read 2 (D00743:144:CAAWNANXX:2:2114:6124:5965_1:N:0:TGACCA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-159_S6_L002_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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam: 6380873 Total number duplicated alignments removed: 1736608 (27.22%) Duplicated alignments were found at: 1097543 different position(s) Total count of deduplicated leftover sequences: 4644265 (72.78% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 4644265 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4644265 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:2203:9947:73882_1:N:0:ACAGTG) and Read 2 (D00743:144:CAAWNANXX:2:1307:6059:31093_1:N:0:ACAGTG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-160_S7_L002_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-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam: 12255648 Total number duplicated alignments removed: 3263582 (26.63%) Duplicated alignments were found at: 1915571 different position(s) Total count of deduplicated leftover sequences: 8992066 (73.37% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-161_S8_L002_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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam: 8593705 Total number duplicated alignments removed: 2262879 (26.33%) Duplicated alignments were found at: 1443182 different position(s) Total count of deduplicated leftover sequences: 6330826 (73.67% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6330826 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6330826 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:2213:6204:79211_1:N:0:CAGATC) and Read 2 (D00743:144:CAAWNANXX:2:2310:2740:2272_1:N:0:CAGATC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-162_S9_L002_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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam: 8267039 Total number duplicated alignments removed: 1883875 (22.79%) Duplicated alignments were found at: 1160963 different position(s) Total count of deduplicated leftover sequences: 6383164 (77.21% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6383164 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6383164 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:1215:10892:37397_1:N:0:ACTTGA) and Read 2 (D00743:144:CAAWNANXX:2:1305:3397:70220_1:N:0:ACTTGA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-167_S10_L002_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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam: 10438000 Total number duplicated alignments removed: 2802912 (26.85%) Duplicated alignments were found at: 1823622 different position(s) Total count of deduplicated leftover sequences: 7635088 (73.15% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 7635088 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 7635088 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:1310:6688:21331_1:N:0:GATCAG) and Read 2 (D00743:144:CAAWNANXX:2:1207:6177:12959_1:N:0:GATCAG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-168_S11_L002_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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam: 8967128 Total number duplicated alignments removed: 2474742 (27.60%) Duplicated alignments were found at: 1499379 different position(s) Total count of deduplicated leftover sequences: 6492386 (72.40% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6492386 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6492386 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:1307:2279:49667_1:N:0:TAGCTT) and Read 2 (D00743:144:CAAWNANXX:2:1215:15461:33127_1:N:0:TAGCTT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-169_S12_L002_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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam: 8408055 Total number duplicated alignments removed: 1984624 (23.60%) Duplicated alignments were found at: 1201335 different position(s) Total count of deduplicated leftover sequences: 6423431 (76.40% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6423431 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6423431 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:1201:14310:12919_1:N:0:GGCTAC) and Read 2 (D00743:144:CAAWNANXX:2:2214:17656:39034_1:N:0:GGCTAC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-170_S13_L002_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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam: 10233760 Total number duplicated alignments removed: 2436682 (23.81%) Duplicated alignments were found at: 1417870 different position(s) Total count of deduplicated leftover sequences: 7797078 (76.19% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 7797078 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 7797078 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:2:2207:5907:101279_1:N:0:CTTGTA) and Read 2 (D00743:144:CAAWNANXX:2:1103:15942:9031_1:N:0:CTTGTA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 7924620 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 7924620 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:1105:6703:51813_1:N:0:ATCACG) and Read 2 (D00743:144:CAAWNANXX:3:2315:11115:25017_1:N:0:ATCACG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 10094686 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 10094686 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:2314:7907:24066_1:N:0:CGATGT) and Read 2 (D00743:144:CAAWNANXX:3:1312:14459:67025_1:N:0:CGATGT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 8210265 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 8210265 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:1311:7509:83845_1:N:0:TTAGGC) and Read 2 (D00743:144:CAAWNANXX:3:2306:17317:37206_1:N:0:TTAGGC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 10266522 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 10266522 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:2202:5644:19625_1:N:0:TGACCA) and Read 2 (D00743:144:CAAWNANXX:3:1211:8945:3019_1:N:0:TGACCA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6296462 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6296462 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:2312:11350:68668_1:N:0:ACAGTG) and Read 2 (D00743:144:CAAWNANXX:3:1114:16469:5790_1:N:0:ACAGTG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 2766273 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 2766273 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:2210:4213:97342_1:N:0:GCCAAT) and Read 2 (D00743:144:CAAWNANXX:3:2108:15810:20101_1:N:0:GCCAAT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 7098905 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 7098905 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:1105:10853:86830_1:N:0:CAGATC) and Read 2 (D00743:144:CAAWNANXX:3:1116:11775:76060_1:N:0:CAGATC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6192833 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6192833 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:1202:19271:43800_1:N:0:ACTTGA) and Read 2 (D00743:144:CAAWNANXX:3:2309:1983:22300_1:N:0:ACTTGA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 8170923 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 8170923 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:1107:8187:12957_1:N:0:GATCAG) and Read 2 (D00743:144:CAAWNANXX:3:1109:1619:39392_1:N:0:GATCAG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 9000946 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 9000946 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:1103:16686:67988_1:N:0:TAGCTT) and Read 2 (D00743:144:CAAWNANXX:3:1314:7180:61852_1:N:0:TAGCTT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 4367077 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4367077 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:1315:11185:46712_1:N:0:GGCTAC) and Read 2 (D00743:144:CAAWNANXX:3:2303:7466:11414_1:N:0:GGCTAC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) 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:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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" Processing paired-end Bismark output file(s) (SAM format): EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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! Output file is: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 7500987 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 7500987 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -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" Processing paired-end Bismark output file(s) (SAM format): EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:3:1106:1618:55266_1:N:0:CTTGTA) and Read 2 (D00743:144:CAAWNANXX:3:2309:19485:5440_1:N:0:CTTGTA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-205_S26_L004_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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam: 6323590 Total number duplicated alignments removed: 1603675 (25.36%) Duplicated alignments were found at: 963679 different position(s) Total count of deduplicated leftover sequences: 4719915 (74.64% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 4719915 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4719915 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:2112:19485:7663_1:N:0:ATCACG) and Read 2 (D00743:144:CAAWNANXX:4:1311:6675:29159_1:N:0:ATCACG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-206_S27_L004_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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam: 8694087 Total number duplicated alignments removed: 1956411 (22.50%) Duplicated alignments were found at: 1112526 different position(s) Total count of deduplicated leftover sequences: 6737676 (77.50% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6737676 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6737676 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:2215:7389:91773_1:N:0:CGATGT) and Read 2 (D00743:144:CAAWNANXX:4:2310:18443:36156_1:N:0:CGATGT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-208_S28_L004_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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam: 11240945 Total number duplicated alignments removed: 2599604 (23.13%) Duplicated alignments were found at: 1452536 different position(s) Total count of deduplicated leftover sequences: 8641341 (76.87% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 8641341 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 8641341 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:2104:9275:7034_1:N:0:TTAGGC) and Read 2 (D00743:144:CAAWNANXX:4:2312:11867:9624_1:N:0:TTAGGC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-209_S29_L004_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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam: 12390014 Total number duplicated alignments removed: 3444505 (27.80%) Duplicated alignments were found at: 2000861 different position(s) Total count of deduplicated leftover sequences: 8945509 (72.20% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 8945509 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 8945509 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:1203:20941:96387_1:N:0:TGACCA) and Read 2 (D00743:144:CAAWNANXX:4:1106:16160:76631_1:N:0:TGACCA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-214_S30_L004_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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam: 11468068 Total number duplicated alignments removed: 2764190 (24.10%) Duplicated alignments were found at: 1689980 different position(s) Total count of deduplicated leftover sequences: 8703878 (75.90% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 8703878 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 8703878 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:1108:12036:88960_1:N:0:ACAGTG) and Read 2 (D00743:144:CAAWNANXX:4:2207:8747:63844_1:N:0:ACAGTG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-215_S31_L004_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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam: 8898557 Total number duplicated alignments removed: 2505655 (28.16%) Duplicated alignments were found at: 1529678 different position(s) Total count of deduplicated leftover sequences: 6392902 (71.84% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6392902 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6392902 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:2312:2439:16444_1:N:0:GCCAAT) and Read 2 (D00743:144:CAAWNANXX:4:2303:13116:33754_1:N:0:GCCAAT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-220_S32_L004_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-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam: 6443740 Total number duplicated alignments removed: 2081383 (32.30%) Duplicated alignments were found at: 1265421 different position(s) Total count of deduplicated leftover sequences: 4362357 (67.70% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 4362357 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4362357 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:1107:7487:45248_1:N:0:CAGATC) and Read 2 (D00743:144:CAAWNANXX:4:2315:9207:23649_1:N:0:CAGATC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-221_S33_L004_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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam: 6871475 Total number duplicated alignments removed: 1959853 (28.52%) Duplicated alignments were found at: 1245701 different position(s) Total count of deduplicated leftover sequences: 4911622 (71.48% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 4911622 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4911622 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:2105:3236:72949_1:N:0:ACTTGA) and Read 2 (D00743:144:CAAWNANXX:4:1208:10550:48769_1:N:0:ACTTGA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-226_S34_L004_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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam: 4644692 Total number duplicated alignments removed: 1206577 (25.98%) Duplicated alignments were found at: 766007 different position(s) Total count of deduplicated leftover sequences: 3438115 (74.02% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 3438115 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 3438115 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:2107:13947:24670_1:N:0:GATCAG) and Read 2 (D00743:144:CAAWNANXX:4:2112:4185:67344_1:N:0:GATCAG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-227_S35_L004_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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam: 5777318 Total number duplicated alignments removed: 1567966 (27.14%) Duplicated alignments were found at: 1031120 different position(s) Total count of deduplicated leftover sequences: 4209352 (72.86% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 4209352 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4209352 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:1202:10515:62954_1:N:0:TAGCTT) and Read 2 (D00743:144:CAAWNANXX:4:2207:13085:44729_1:N:0:TAGCTT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-229_S36_L004_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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam: 8020237 Total number duplicated alignments removed: 1983971 (24.74%) Duplicated alignments were found at: 1179618 different position(s) Total count of deduplicated leftover sequences: 6036266 (75.26% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6036266 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6036266 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:1114:3827:80172_1:N:0:GGCTAC) and Read 2 (D00743:144:CAAWNANXX:4:1216:9392:92633_1:N:0:GGCTAC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-230_S37_L004_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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam: 11206077 Total number duplicated alignments removed: 3923633 (35.01%) Duplicated alignments were found at: 2312024 different position(s) Total count of deduplicated leftover sequences: 7282444 (64.99% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 7282444 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 7282444 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:4:1308:5514:17531_1:N:0:CTTGTA) and Read 2 (D00743:144:CAAWNANXX:4:2307:15650:87137_1:N:0:CTTGTA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam: 10110532 Total number duplicated alignments removed: 3711212 (36.71%) Duplicated alignments were found at: 2206337 different position(s) Total count of deduplicated leftover sequences: 6399320 (63.29% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6399320 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6399320 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:5:1206:11465:41955_1:N:0:ATCACG) and Read 2 (D00743:144:CAAWNANXX:5:2307:19621:9035_1:N:0:ATCACG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam: 13173399 Total number duplicated alignments removed: 4597382 (34.90%) Duplicated alignments were found at: 2730000 different position(s) Total count of deduplicated leftover sequences: 8576017 (65.10% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 8576017 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 8576017 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:5:1305:11362:17544_1:N:0:CGATGT) and Read 2 (D00743:144:CAAWNANXX:5:1311:10105:47869_1:N:0:CGATGT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam: 10112774 Total number duplicated alignments removed: 3692163 (36.51%) Duplicated alignments were found at: 2223544 different position(s) Total count of deduplicated leftover sequences: 6420611 (63.49% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 6420611 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 6420611 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:5:1201:3456:8313_1:N:0:TGACCA) and Read 2 (D00743:144:CAAWNANXX:5:2112:16537:54443_1:N:0:TGACCA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) Processing paired-end Bismark output file(s) (SAM format): EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam: 6084804 Total number duplicated alignments removed: 2053760 (33.75%) Duplicated alignments were found at: 1305099 different position(s) Total count of deduplicated leftover sequences: 4031044 (66.25% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam: 4031044 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4031044 (100.00% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Scaffold_01 LN:89643857 skipping header line: @SQ SN:Scaffold_02 LN:69596280 skipping header line: @SQ SN:Scaffold_03 LN:57743597 skipping header line: @SQ SN:Scaffold_04 LN:65288255 skipping header line: @SQ SN:Scaffold_05 LN:67248332 skipping header line: @SQ SN:Scaffold_06 LN:61759565 skipping header line: @SQ SN:Scaffold_07 LN:43120122 skipping header line: @SQ SN:Scaffold_08 LN:61151155 skipping header line: @SQ SN:Scaffold_09 LN:38581958 skipping header line: @SQ SN:Scaffold_10 LN:53961475 skipping header line: @SQ SN:Scaffold_11 LN:51449921 skipping header line: @SQ SN:Scaffold_12 LN:50438331 skipping header line: @SQ SN:Scaffold_13 LN:44396874 skipping header line: @SQ SN:Scaffold_14 LN:45393038 skipping header line: @SQ SN:Scaffold_15 LN:47938513 skipping header line: @SQ SN:Scaffold_16 LN:31980953 skipping header line: @SQ SN:Scaffold_17 LN:34923512 skipping header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam<< for signs of file truncation... Now testing Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam for positional sorting (which would be bad...) The IDs of Read 1 (D00743:144:CAAWNANXX:5:2105:15741:45562_1:N:0:ACTTGA) and Read 2 (D00743:144:CAAWNANXX:5:2203:12381:69873_1:N:0:ACTTGA) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n) *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/scrubbed/sr320/1218') Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '75%'. Temporary directory used for sorting is the output directory Checking file >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 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Processed lines: 5500000 Processed lines: 6500000 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 Processed lines: 6000000 Processed lines: 7000000 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: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7500000 Finished processing child process. Exiting.. 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 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7835836 lines in total Total number of methylation call strings processed: 15671672 Final Cytosine Methylation Report ================================= Total number of C's analysed: 183501406 Total methylated C's in CpG context: 6658001 Total methylated C's in CHG context: 852229 Total methylated C's in CHH context: 1574350 Total C to T conversions in CpG context: 18809270 Total C to T conversions in CHG context: 36884209 Total C to T conversions in CHH context: 118723347 C methylated in CpG context: 26.1% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed 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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: 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.. 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-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 7835836 lines in total Total number of methylation call strings processed: 15671672 Final Cytosine Methylation Report ================================= Total number of C's analysed: 183501406 Total methylated C's in CpG context: 6658001 Total methylated C's in CHG context: 852229 Total methylated C's in CHH context: 1574350 Total C to T conversions in CpG context: 18809270 Total C to T conversions in CHG context: 36884209 Total C to T conversions in CHH context: 118723347 C methylated in CpG context: 26.1% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 11500000 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-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 11613745 lines in total Total number of methylation call strings processed: 23227490 Final Cytosine Methylation Report ================================= Total number of C's analysed: 256681996 Total methylated C's in CpG context: 10137100 Total methylated C's in CHG context: 1260299 Total methylated C's in CHH context: 2323535 Total C to T conversions in CpG context: 24263858 Total C to T conversions in CHG context: 51430750 Total C to T conversions in CHH context: 167266454 C methylated in CpG context: 29.5% C methylated in CHG context: 2.4% C methylated in CHH context: 1.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed 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lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Finished processing child process. Exiting.. Processed lines: 11500000 Processed lines: 11500000 Finished processing child process. Exiting.. Processed lines: 11500000 Finished processing child process. Exiting.. Processed lines: 11500000 Processed lines: 11500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 11500000 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-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 11613745 lines in total Total number of methylation call strings processed: 23227490 Final Cytosine Methylation Report ================================= Total number of C's analysed: 256681996 Total methylated C's in CpG context: 10137100 Total methylated C's in CHG context: 1260299 Total methylated C's in CHH context: 2323535 Total C to T conversions in CpG context: 24263858 Total C to T conversions in CHG context: 51430750 Total C to T conversions in CHH context: 167266454 C methylated in CpG context: 29.5% C methylated in CHG context: 2.4% C methylated in CHH context: 1.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10466822 lines in total Total number of methylation call strings processed: 20933644 Final Cytosine Methylation Report ================================= Total number of C's analysed: 231214858 Total methylated C's in CpG context: 8681437 Total methylated C's in CHG context: 1156157 Total methylated C's in CHH context: 1936920 Total C to T conversions in CpG context: 22978618 Total C to T conversions in CHG context: 46067897 Total C to T conversions in CHH context: 150393829 C methylated in CpG context: 27.4% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed 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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 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: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 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 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.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 10466822 lines in total Total number of methylation call strings processed: 20933644 Final Cytosine Methylation Report ================================= Total number of C's analysed: 231214858 Total methylated C's in CpG context: 8681437 Total methylated C's in CHG context: 1156157 Total methylated C's in CHH context: 1936920 Total C to T conversions in CpG context: 22978618 Total C to T conversions in CHG context: 46067897 Total C to T conversions in CHH context: 150393829 C methylated in CpG context: 27.4% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9854743 lines in total Total number of methylation call strings processed: 19709486 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224084049 Total methylated C's in CpG context: 8423482 Total methylated C's in CHG context: 1104529 Total methylated C's in CHH context: 1867274 Total C to T conversions in CpG context: 22028913 Total C to T conversions in CHG context: 44713152 Total C to T conversions in CHH context: 145946699 C methylated in CpG context: 27.7% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed 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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 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: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 9854743 lines in total Total number of methylation call strings processed: 19709486 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224084049 Total methylated C's in CpG context: 8423482 Total methylated C's in CHG context: 1104529 Total methylated C's in CHH context: 1867274 Total C to T conversions in CpG context: 22028913 Total C to T conversions in CHG context: 44713152 Total C to T conversions in CHH context: 145946699 C methylated in CpG context: 27.7% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 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: 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9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 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 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.. 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-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10413822 lines in total Total number of methylation call strings processed: 20827644 Final Cytosine Methylation Report ================================= Total number of C's analysed: 243953258 Total methylated C's in CpG context: 8558544 Total methylated C's in CHG context: 1135855 Total methylated C's in CHH context: 2017566 Total C to T conversions in CpG context: 25838202 Total C to T conversions in CHG context: 48531203 Total C to T conversions in CHH context: 157871888 C methylated in CpG context: 24.9% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed 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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 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: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 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 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.. 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-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 10413822 lines in total Total number of methylation call strings processed: 20827644 Final Cytosine Methylation Report ================================= Total number of C's analysed: 243953258 Total methylated C's in CpG context: 8558544 Total methylated C's in CHG context: 1135855 Total methylated C's in CHH context: 2017566 Total C to T conversions in CpG context: 25838202 Total C to T conversions in CHG context: 48531203 Total C to T conversions in CHH context: 157871888 C methylated in CpG context: 24.9% C methylated in CHG context: 2.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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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-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9470106 lines in total Total number of methylation call strings processed: 18940212 Final Cytosine Methylation Report ================================= Total number of C's analysed: 217946429 Total methylated C's in CpG context: 8187042 Total methylated C's in CHG context: 1062536 Total methylated C's in CHH context: 1832611 Total C to T conversions in CpG context: 21761145 Total C to T conversions in CHG context: 43433409 Total C to T conversions in CHH context: 141669686 C methylated in CpG context: 27.3% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 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: 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8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 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: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 9470106 lines in total Total number of methylation call strings processed: 18940212 Final Cytosine Methylation Report ================================= Total number of C's analysed: 217946429 Total methylated C's in CpG context: 8187042 Total methylated C's in CHG context: 1062536 Total methylated C's in CHH context: 1832611 Total C to T conversions in CpG context: 21761145 Total C to T conversions in CHG context: 43433409 Total C to T conversions in CHH context: 141669686 C methylated in CpG context: 27.3% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 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: 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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.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8450079 lines in total Total number of methylation call strings processed: 16900158 Final Cytosine Methylation Report ================================= Total number of C's analysed: 196938082 Total methylated C's in CpG context: 7564205 Total methylated C's in CHG context: 967557 Total methylated C's in CHH context: 1694338 Total C to T conversions in CpG context: 19544907 Total C to T conversions in CHG context: 39233900 Total C to T conversions in CHH context: 127933175 C methylated in CpG context: 27.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed 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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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 8450079 lines in total Total number of methylation call strings processed: 16900158 Final Cytosine Methylation Report ================================= Total number of C's analysed: 196938082 Total methylated C's in CpG context: 7564205 Total methylated C's in CHG context: 967557 Total methylated C's in CHH context: 1694338 Total C to T conversions in CpG context: 19544907 Total C to T conversions in CHG context: 39233900 Total C to T conversions in CHH context: 127933175 C methylated in CpG context: 27.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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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-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9300124 lines in total Total number of methylation call strings processed: 18600248 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215109906 Total methylated C's in CpG context: 8244675 Total methylated C's in CHG context: 1071477 Total methylated C's in CHH context: 1772832 Total C to T conversions in CpG context: 21307910 Total C to T conversions in CHG context: 42824701 Total C to T conversions in CHH context: 139888311 C methylated in CpG context: 27.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed 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lines: 9000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 9300124 lines in total Total number of methylation call strings processed: 18600248 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215109906 Total methylated C's in CpG context: 8244675 Total methylated C's in CHG context: 1071477 Total methylated C's in CHH context: 1772832 Total C to T conversions in CpG context: 21307910 Total C to T conversions in CHG context: 42824701 Total C to T conversions in CHH context: 139888311 C methylated in CpG context: 27.9% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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Exiting.. Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10559504 lines in total Total number of methylation call strings processed: 21119008 Final Cytosine Methylation Report ================================= Total number of C's analysed: 225992948 Total methylated C's in CpG context: 9046557 Total methylated C's in CHG context: 1202237 Total methylated C's in CHH context: 2001278 Total C to T conversions in CpG context: 21842118 Total C to T conversions in CHG context: 45361388 Total C to T conversions in CHH context: 146539370 C methylated in CpG context: 29.3% C methylated in CHG context: 2.6% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed 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lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 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 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10500000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 10559504 lines in total Total number of methylation call strings processed: 21119008 Final Cytosine Methylation Report ================================= Total number of C's analysed: 225992948 Total methylated C's in CpG context: 9046557 Total methylated C's in CHG context: 1202237 Total methylated C's in CHH context: 2001278 Total C to T conversions in CpG context: 21842118 Total C to T conversions in CHG context: 45361388 Total C to T conversions in CHH context: 146539370 C methylated in CpG context: 29.3% C methylated in CHG context: 2.6% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 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9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 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 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.. 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-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10289878 lines in total Total number of methylation call strings processed: 20579756 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222520026 Total methylated C's in CpG context: 8205504 Total methylated C's in CHG context: 1105916 Total methylated C's in CHH context: 1849444 Total C to T conversions in CpG context: 22514794 Total C to T conversions in CHG context: 44690621 Total C to T conversions in CHH context: 144153747 C methylated in CpG context: 26.7% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed 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lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 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 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.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 10289878 lines in total Total number of methylation call strings processed: 20579756 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222520026 Total methylated C's in CpG context: 8205504 Total methylated C's in CHG context: 1105916 Total methylated C's in CHH context: 1849444 Total C to T conversions in CpG context: 22514794 Total C to T conversions in CHG context: 44690621 Total C to T conversions in CHH context: 144153747 C methylated in CpG context: 26.7% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 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: 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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-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7896079 lines in total Total number of methylation call strings processed: 15792158 Final Cytosine Methylation Report ================================= Total number of C's analysed: 180013500 Total methylated C's in CpG context: 6934397 Total methylated C's in CHG context: 872844 Total methylated C's in CHH context: 1579087 Total C to T conversions in CpG context: 17647358 Total C to T conversions in CHG context: 35893215 Total C to T conversions in CHH context: 117086599 C methylated in CpG context: 28.2% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 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 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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: 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.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 7896079 lines in total Total number of methylation call strings processed: 15792158 Final Cytosine Methylation Report ================================= Total number of C's analysed: 180013500 Total methylated C's in CpG context: 6934397 Total methylated C's in CHG context: 872844 Total methylated C's in CHH context: 1579087 Total C to T conversions in CpG context: 17647358 Total C to T conversions in CHG context: 35893215 Total C to T conversions in CHH context: 117086599 C methylated in CpG context: 28.2% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 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: 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8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 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: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9355933 lines in total Total number of methylation call strings processed: 18711866 Final Cytosine Methylation Report ================================= Total number of C's analysed: 214985786 Total methylated C's in CpG context: 8245428 Total methylated C's in CHG context: 1047240 Total methylated C's in CHH context: 1811240 Total C to T conversions in CpG context: 21238566 Total C to T conversions in CHG context: 42806098 Total C to T conversions in CHH context: 139837214 C methylated in CpG context: 28.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-145_S38_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed 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lines: 8000000 Processed lines: 8500000 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: 9000000 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: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 9355933 lines in total Total number of methylation call strings processed: 18711866 Final Cytosine Methylation Report ================================= Total number of C's analysed: 214985786 Total methylated C's in CpG context: 8245428 Total methylated C's in CHG context: 1047240 Total methylated C's in CHH context: 1811240 Total C to T conversions in CpG context: 21238566 Total C to T conversions in CHG context: 42806098 Total C to T conversions in CHH context: 139837214 C methylated in CpG context: 28.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-151_S2_L002_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-151_S2_L002_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-151_S2_L002_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-151_S2_L002_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-151_S2_L002_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-151_S2_L002_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-151_S2_L002_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-151_S2_L002_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-151_S2_L002_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-151_S2_L002_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-151_S2_L002_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-151_S2_L002_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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_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 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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 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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7210277 lines in total Total number of methylation call strings processed: 14420554 Final Cytosine Methylation Report ================================= Total number of C's analysed: 154371720 Total methylated C's in CpG context: 6619617 Total methylated C's in CHG context: 739999 Total methylated C's in CHH context: 1943298 Total C to T conversions in CpG context: 14863708 Total C to T conversions in CHG context: 32156644 Total C to T conversions in CHH context: 98048454 C methylated in CpG context: 30.8% C methylated in CHG context: 2.2% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-151_S2_L002_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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-151_S2_L002_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/sr320/1218/CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-151_S2_L002_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-151_S2_L002_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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-151_S2_L002_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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_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: 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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 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 7210277 lines in total Total number of methylation call strings processed: 14420554 Final Cytosine Methylation Report ================================= Total number of C's analysed: 154371720 Total methylated C's in CpG context: 6619617 Total methylated C's in CHG context: 739999 Total methylated C's in CHH context: 1943298 Total C to T conversions in CpG context: 14863708 Total C to T conversions in CHG context: 32156644 Total C to T conversions in CHH context: 98048454 C methylated in CpG context: 30.8% C methylated in CHG context: 2.2% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-152_S3_L002_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-152_S3_L002_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-152_S3_L002_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-152_S3_L002_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-152_S3_L002_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-152_S3_L002_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-152_S3_L002_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-152_S3_L002_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-152_S3_L002_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-152_S3_L002_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-152_S3_L002_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-152_S3_L002_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-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-152_S3_L002_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_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 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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.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8409770 lines in total Total number of methylation call strings processed: 16819540 Final Cytosine Methylation Report ================================= Total number of C's analysed: 181742375 Total methylated C's in CpG context: 7874020 Total methylated C's in CHG context: 929405 Total methylated C's in CHH context: 2251146 Total C to T conversions in CpG context: 16740253 Total C to T conversions in CHG context: 36920601 Total C to T conversions in CHH context: 117026950 C methylated in CpG context: 32.0% C methylated in CHG context: 2.5% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-152_S3_L002_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-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-152_S3_L002_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/sr320/1218/CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-152_S3_L002_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-152_S3_L002_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-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-152_S3_L002_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-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_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 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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.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 8409770 lines in total Total number of methylation call strings processed: 16819540 Final Cytosine Methylation Report ================================= Total number of C's analysed: 181742375 Total methylated C's in CpG context: 7874020 Total methylated C's in CHG context: 929405 Total methylated C's in CHH context: 2251146 Total C to T conversions in CpG context: 16740253 Total C to T conversions in CHG context: 36920601 Total C to T conversions in CHH context: 117026950 C methylated in CpG context: 32.0% C methylated in CHG context: 2.5% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-153_S4_L002_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-153_S4_L002_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-153_S4_L002_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-153_S4_L002_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-153_S4_L002_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-153_S4_L002_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-153_S4_L002_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-153_S4_L002_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-153_S4_L002_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-153_S4_L002_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-153_S4_L002_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-153_S4_L002_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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-153_S4_L002_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_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 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Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Finished processing child process. Exiting.. Processed lines: 6500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 6500000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6699555 lines in total Total number of methylation call strings processed: 13399110 Final Cytosine Methylation Report ================================= Total number of C's analysed: 136016129 Total methylated C's in CpG context: 5750945 Total methylated C's in CHG context: 699624 Total methylated C's in CHH context: 1733351 Total C to T conversions in CpG context: 13021245 Total C to T conversions in CHG context: 28351144 Total C to T conversions in CHH context: 86459820 C methylated in CpG context: 30.6% C methylated in CHG context: 2.4% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-153_S4_L002_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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-153_S4_L002_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/sr320/1218/CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-153_S4_L002_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-153_S4_L002_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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-153_S4_L002_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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_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 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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: 6500000 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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6699555 lines in total Total number of methylation call strings processed: 13399110 Final Cytosine Methylation Report ================================= Total number of C's analysed: 136016129 Total methylated C's in CpG context: 5750945 Total methylated C's in CHG context: 699624 Total methylated C's in CHH context: 1733351 Total C to T conversions in CpG context: 13021245 Total C to T conversions in CHG context: 28351144 Total C to T conversions in CHH context: 86459820 C methylated in CpG context: 30.6% C methylated in CHG context: 2.4% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-154_S5_L002_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-154_S5_L002_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-154_S5_L002_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-154_S5_L002_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-154_S5_L002_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-154_S5_L002_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-154_S5_L002_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-154_S5_L002_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-154_S5_L002_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-154_S5_L002_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-154_S5_L002_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-154_S5_L002_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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-154_S5_L002_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_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 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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 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.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6769523 lines in total Total number of methylation call strings processed: 13539046 Final Cytosine Methylation Report ================================= Total number of C's analysed: 142831749 Total methylated C's in CpG context: 5958725 Total methylated C's in CHG context: 672814 Total methylated C's in CHH context: 1876297 Total C to T conversions in CpG context: 13541358 Total C to T conversions in CHG context: 29209282 Total C to T conversions in CHH context: 91573273 C methylated in CpG context: 30.6% 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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-154_S5_L002_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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-154_S5_L002_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/sr320/1218/CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-154_S5_L002_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-154_S5_L002_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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-154_S5_L002_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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_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 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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: 6500000 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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6769523 lines in total Total number of methylation call strings processed: 13539046 Final Cytosine Methylation Report ================================= Total number of C's analysed: 142831749 Total methylated C's in CpG context: 5958725 Total methylated C's in CHG context: 672814 Total methylated C's in CHH context: 1876297 Total C to T conversions in CpG context: 13541358 Total C to T conversions in CHG context: 29209282 Total C to T conversions in CHH context: 91573273 C methylated in CpG context: 30.6% 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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-159_S6_L002_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-159_S6_L002_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-159_S6_L002_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-159_S6_L002_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-159_S6_L002_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-159_S6_L002_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-159_S6_L002_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-159_S6_L002_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-159_S6_L002_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-159_S6_L002_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-159_S6_L002_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-159_S6_L002_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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_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 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 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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4644265 lines in total Total number of methylation call strings processed: 9288530 Final Cytosine Methylation Report ================================= Total number of C's analysed: 99137282 Total methylated C's in CpG context: 4217985 Total methylated C's in CHG context: 535634 Total methylated C's in CHH context: 1932988 Total C to T conversions in CpG context: 9196803 Total C to T conversions in CHG context: 20037165 Total C to T conversions in CHH context: 63216707 C methylated in CpG context: 31.4% C methylated in CHG context: 2.6% C methylated in CHH context: 3.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-159_S6_L002_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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-159_S6_L002_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/sr320/1218/CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-159_S6_L002_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-159_S6_L002_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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-159_S6_L002_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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_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 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 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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 4644265 lines in total Total number of methylation call strings processed: 9288530 Final Cytosine Methylation Report ================================= Total number of C's analysed: 99137282 Total methylated C's in CpG context: 4217985 Total methylated C's in CHG context: 535634 Total methylated C's in CHH context: 1932988 Total C to T conversions in CpG context: 9196803 Total C to T conversions in CHG context: 20037165 Total C to T conversions in CHH context: 63216707 C methylated in CpG context: 31.4% C methylated in CHG context: 2.6% C methylated in CHH context: 3.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-160_S7_L002_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-160_S7_L002_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-160_S7_L002_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-160_S7_L002_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-160_S7_L002_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-160_S7_L002_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-160_S7_L002_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-160_S7_L002_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-160_S7_L002_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-160_S7_L002_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-160_S7_L002_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-160_S7_L002_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-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-160_S7_L002_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_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 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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 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 Processed lines: 8000000 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: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8992066 lines in total Total number of methylation call strings processed: 17984132 Final Cytosine Methylation Report ================================= Total number of C's analysed: 176538868 Total methylated C's in CpG context: 7344361 Total methylated C's in CHG context: 912079 Total methylated C's in CHH context: 2297548 Total C to T conversions in CpG context: 16933790 Total C to T conversions in CHG context: 36262599 Total C to T conversions in CHH context: 112788491 C methylated in CpG context: 30.3% C methylated in CHG context: 2.5% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-160_S7_L002_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-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-160_S7_L002_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/sr320/1218/CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-160_S7_L002_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-160_S7_L002_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-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-160_S7_L002_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-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-161_S8_L002_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-161_S8_L002_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-161_S8_L002_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-161_S8_L002_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-161_S8_L002_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-161_S8_L002_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-161_S8_L002_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-161_S8_L002_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-161_S8_L002_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-161_S8_L002_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-161_S8_L002_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-161_S8_L002_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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-161_S8_L002_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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-161_S8_L002_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_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 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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6330826 lines in total Total number of methylation call strings processed: 12661652 Final Cytosine Methylation Report ================================= Total number of C's analysed: 124508835 Total methylated C's in CpG context: 4903316 Total methylated C's in CHG context: 619102 Total methylated C's in CHH context: 1795108 Total C to T conversions in CpG context: 12097133 Total C to T conversions in CHG context: 25334277 Total C to T conversions in CHH context: 79759899 C methylated in CpG context: 28.8% C methylated in CHG context: 2.4% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-161_S8_L002_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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-161_S8_L002_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/sr320/1218/CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-161_S8_L002_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-161_S8_L002_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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-161_S8_L002_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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_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 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.. Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6330826 lines in total Total number of methylation call strings processed: 12661652 Final Cytosine Methylation Report ================================= Total number of C's analysed: 124508835 Total methylated C's in CpG context: 4903316 Total methylated C's in CHG context: 619102 Total methylated C's in CHH context: 1795108 Total C to T conversions in CpG context: 12097133 Total C to T conversions in CHG context: 25334277 Total C to T conversions in CHH context: 79759899 C methylated in CpG context: 28.8% C methylated in CHG context: 2.4% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-162_S9_L002_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-162_S9_L002_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-162_S9_L002_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-162_S9_L002_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-162_S9_L002_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-162_S9_L002_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-162_S9_L002_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-162_S9_L002_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-162_S9_L002_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-162_S9_L002_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-162_S9_L002_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-162_S9_L002_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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-162_S9_L002_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_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 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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6383164 lines in total Total number of methylation call strings processed: 12766328 Final Cytosine Methylation Report ================================= Total number of C's analysed: 122908719 Total methylated C's in CpG context: 4824979 Total methylated C's in CHG context: 612515 Total methylated C's in CHH context: 1827593 Total C to T conversions in CpG context: 12090566 Total C to T conversions in CHG context: 25238601 Total C to T conversions in CHH context: 78314465 C methylated in CpG context: 28.5% C methylated in CHG context: 2.4% C methylated in CHH context: 2.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-162_S9_L002_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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-162_S9_L002_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/sr320/1218/CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-162_S9_L002_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-162_S9_L002_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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-162_S9_L002_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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_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 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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6383164 lines in total Total number of methylation call strings processed: 12766328 Final Cytosine Methylation Report ================================= Total number of C's analysed: 122908719 Total methylated C's in CpG context: 4824979 Total methylated C's in CHG context: 612515 Total methylated C's in CHH context: 1827593 Total C to T conversions in CpG context: 12090566 Total C to T conversions in CHG context: 25238601 Total C to T conversions in CHH context: 78314465 C methylated in CpG context: 28.5% C methylated in CHG context: 2.4% C methylated in CHH context: 2.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-167_S10_L002_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-167_S10_L002_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-167_S10_L002_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-167_S10_L002_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-167_S10_L002_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-167_S10_L002_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-167_S10_L002_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-167_S10_L002_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-167_S10_L002_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-167_S10_L002_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-167_S10_L002_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-167_S10_L002_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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-167_S10_L002_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_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: 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Exiting.. Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. 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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7635088 lines in total Total number of methylation call strings processed: 15270176 Final Cytosine Methylation Report ================================= Total number of C's analysed: 169475057 Total methylated C's in CpG context: 6721143 Total methylated C's in CHG context: 1081552 Total methylated C's in CHH context: 3482873 Total C to T conversions in CpG context: 15986854 Total C to T conversions in CHG context: 34252524 Total C to T conversions in CHH context: 107950111 C methylated in CpG context: 29.6% C methylated in CHG context: 3.1% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-167_S10_L002_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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-167_S10_L002_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/sr320/1218/CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-167_S10_L002_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-167_S10_L002_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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-167_S10_L002_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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_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 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Exiting.. Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 7635088 lines in total Total number of methylation call strings processed: 15270176 Final Cytosine Methylation Report ================================= Total number of C's analysed: 169475057 Total methylated C's in CpG context: 6721143 Total methylated C's in CHG context: 1081552 Total methylated C's in CHH context: 3482873 Total C to T conversions in CpG context: 15986854 Total C to T conversions in CHG context: 34252524 Total C to T conversions in CHH context: 107950111 C methylated in CpG context: 29.6% C methylated in CHG context: 3.1% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-168_S11_L002_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-168_S11_L002_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-168_S11_L002_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-168_S11_L002_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-168_S11_L002_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-168_S11_L002_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-168_S11_L002_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-168_S11_L002_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-168_S11_L002_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-168_S11_L002_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-168_S11_L002_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-168_S11_L002_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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-168_S11_L002_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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_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: 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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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6492386 lines in total Total number of methylation call strings processed: 12984772 Final Cytosine Methylation Report ================================= Total number of C's analysed: 139836026 Total methylated C's in CpG context: 5749134 Total methylated C's in CHG context: 652679 Total methylated C's in CHH context: 1958750 Total C to T conversions in CpG context: 13380784 Total C to T conversions in CHG context: 28960958 Total C to T conversions in CHH context: 89133721 C methylated in CpG context: 30.1% C methylated in CHG context: 2.2% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-168_S11_L002_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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-168_S11_L002_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/sr320/1218/CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-168_S11_L002_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-168_S11_L002_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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-168_S11_L002_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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_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 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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6492386 lines in total Total number of methylation call strings processed: 12984772 Final Cytosine Methylation Report ================================= Total number of C's analysed: 139836026 Total methylated C's in CpG context: 5749134 Total methylated C's in CHG context: 652679 Total methylated C's in CHH context: 1958750 Total C to T conversions in CpG context: 13380784 Total C to T conversions in CHG context: 28960958 Total C to T conversions in CHH context: 89133721 C methylated in CpG context: 30.1% C methylated in CHG context: 2.2% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-169_S12_L002_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-169_S12_L002_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-169_S12_L002_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-169_S12_L002_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-169_S12_L002_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-169_S12_L002_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-169_S12_L002_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-169_S12_L002_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-169_S12_L002_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-169_S12_L002_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-169_S12_L002_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-169_S12_L002_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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-169_S12_L002_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_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: 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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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6423431 lines in total Total number of methylation call strings processed: 12846862 Final Cytosine Methylation Report ================================= Total number of C's analysed: 127237948 Total methylated C's in CpG context: 5351229 Total methylated C's in CHG context: 663359 Total methylated C's in CHH context: 2095978 Total C to T conversions in CpG context: 12254820 Total C to T conversions in CHG context: 26439097 Total C to T conversions in CHH context: 80433465 C methylated in CpG context: 30.4% C methylated in CHG context: 2.4% C methylated in CHH context: 2.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-169_S12_L002_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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-169_S12_L002_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/sr320/1218/CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-169_S12_L002_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-169_S12_L002_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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-169_S12_L002_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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_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 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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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6423431 lines in total Total number of methylation call strings processed: 12846862 Final Cytosine Methylation Report ================================= Total number of C's analysed: 127237948 Total methylated C's in CpG context: 5351229 Total methylated C's in CHG context: 663359 Total methylated C's in CHH context: 2095978 Total C to T conversions in CpG context: 12254820 Total C to T conversions in CHG context: 26439097 Total C to T conversions in CHH context: 80433465 C methylated in CpG context: 30.4% C methylated in CHG context: 2.4% C methylated in CHH context: 2.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-170_S13_L002_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-170_S13_L002_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-170_S13_L002_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-170_S13_L002_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-170_S13_L002_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-170_S13_L002_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-170_S13_L002_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-170_S13_L002_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-170_S13_L002_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-170_S13_L002_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-170_S13_L002_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-170_S13_L002_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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_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: 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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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7797078 lines in total Total number of methylation call strings processed: 15594156 Final Cytosine Methylation Report ================================= Total number of C's analysed: 151781122 Total methylated C's in CpG context: 5915753 Total methylated C's in CHG context: 746213 Total methylated C's in CHH context: 1797219 Total C to T conversions in CpG context: 15089108 Total C to T conversions in CHG context: 31172597 Total C to T conversions in CHH context: 97060232 C methylated in CpG context: 28.2% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-170_S13_L002_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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-170_S13_L002_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/sr320/1218/CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-170_S13_L002_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-170_S13_L002_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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-170_S13_L002_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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_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: 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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.. 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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 7797078 lines in total Total number of methylation call strings processed: 15594156 Final Cytosine Methylation Report ================================= Total number of C's analysed: 151781122 Total methylated C's in CpG context: 5915753 Total methylated C's in CHG context: 746213 Total methylated C's in CHH context: 1797219 Total C to T conversions in CpG context: 15089108 Total C to T conversions in CHG context: 31172597 Total C to T conversions in CHH context: 97060232 C methylated in CpG context: 28.2% C methylated in CHG context: 2.3% C methylated in CHH context: 1.8% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.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-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... 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 Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. 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 Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. 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 Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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: 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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-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/sr320/1218/CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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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: 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.. 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-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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 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 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 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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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: 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9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 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 Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 Finished processing child process. Exiting.. 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.. 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-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/sr320/1218/CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 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 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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: 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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-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/sr320/1218/CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. 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.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.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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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: 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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.. 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/sr320/1218/CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. 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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 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 Finished processing child process. Exiting.. Processed lines: 10000000 Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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: 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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/sr320/1218/CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. 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.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.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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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 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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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.deduplicated_splitting_report.txt' Merging from these individual files: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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 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 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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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.. 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-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/sr320/1218/CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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.. 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-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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 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 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. 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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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: 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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 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.. 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-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/sr320/1218/CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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 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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 Processed lines: 6000000 Processed lines: 6000000 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: 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 Finished processing child process. Exiting.. 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.. Processed lines: 7000000 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.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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 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. 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. 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. 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. 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. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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: 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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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-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/sr320/1218/CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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 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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 Finished processing child process. Exiting.. Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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: 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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-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/sr320/1218/CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.deduplicated.bam Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. 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.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.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.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.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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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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.. Processed lines: 8000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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 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. 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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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: 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Exiting.. Processed lines: 9000000 Processed lines: 9000000 Finished processing child process. Exiting.. 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 Processed lines: 9000000 Finished processing child process. Exiting.. 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/sr320/1218/CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.deduplicated.bam Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.deduplicated.bam Warning: unable to close filehandle IN properly. 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.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.deduplicated.bam Now reading in Bismark result file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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: 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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 Processed lines: 9000000 Finished processing child process. Exiting.. 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.deduplicated_splitting_report.txt' Merging from these individual files: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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/sr320/1218/CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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.deduplicated_splitting_report.txt' Merging from these individual files: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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: 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Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 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 Now waiting for all child processes to complete 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/sr320/1218/CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/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 ... Checking file >>EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.txt Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.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.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.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.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.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.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.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.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.deduplicated.bam Now reading in Bismark result file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -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 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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: 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 Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 Processed lines: 7500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 7500000 Finished processing child process. Exiting.. Processed lines: 7500000 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 Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated_splitting_report.txt.1.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.txt contains data -> kept CpG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.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.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.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.deduplicated.txt to merged temp file Sorting input file EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.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.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-205_S26_L004_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-205_S26_L004_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-205_S26_L004_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-205_S26_L004_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-205_S26_L004_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-205_S26_L004_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-205_S26_L004_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-205_S26_L004_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-205_S26_L004_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-205_S26_L004_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-205_S26_L004_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-205_S26_L004_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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-205_S26_L004_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_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 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 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 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4719915 lines in total Total number of methylation call strings processed: 9439830 Final Cytosine Methylation Report ================================= Total number of C's analysed: 85575964 Total methylated C's in CpG context: 3859626 Total methylated C's in CHG context: 469729 Total methylated C's in CHH context: 1198594 Total C to T conversions in CpG context: 8425101 Total C to T conversions in CHG context: 17659824 Total C to T conversions in CHH context: 53963090 C methylated in CpG context: 31.4% 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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-205_S26_L004_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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-205_S26_L004_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/sr320/1218/CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-205_S26_L004_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-205_S26_L004_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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-205_S26_L004_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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_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: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 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: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 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.. Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 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: 4500000 Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 4719915 lines in total Total number of methylation call strings processed: 9439830 Final Cytosine Methylation Report ================================= Total number of C's analysed: 85575964 Total methylated C's in CpG context: 3859626 Total methylated C's in CHG context: 469729 Total methylated C's in CHH context: 1198594 Total C to T conversions in CpG context: 8425101 Total C to T conversions in CHG context: 17659824 Total C to T conversions in CHH context: 53963090 C methylated in CpG context: 31.4% 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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-206_S27_L004_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-206_S27_L004_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-206_S27_L004_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-206_S27_L004_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-206_S27_L004_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-206_S27_L004_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-206_S27_L004_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-206_S27_L004_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-206_S27_L004_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-206_S27_L004_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-206_S27_L004_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-206_S27_L004_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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_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: 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6500000 Finished processing child process. Exiting.. Processed lines: 6500000 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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6737676 lines in total Total number of methylation call strings processed: 13475352 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128475689 Total methylated C's in CpG context: 5690111 Total methylated C's in CHG context: 686060 Total methylated C's in CHH context: 1836981 Total C to T conversions in CpG context: 12491913 Total C to T conversions in CHG context: 26714902 Total C to T conversions in CHH context: 81055722 C methylated in CpG context: 31.3% C methylated in CHG context: 2.5% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-206_S27_L004_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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-206_S27_L004_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/sr320/1218/CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-206_S27_L004_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-206_S27_L004_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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-206_S27_L004_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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_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: 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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 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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: 6500000 Processed lines: 6500000 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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6737676 lines in total Total number of methylation call strings processed: 13475352 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128475689 Total methylated C's in CpG context: 5690111 Total methylated C's in CHG context: 686060 Total methylated C's in CHH context: 1836981 Total C to T conversions in CpG context: 12491913 Total C to T conversions in CHG context: 26714902 Total C to T conversions in CHH context: 81055722 C methylated in CpG context: 31.3% C methylated in CHG context: 2.5% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-208_S28_L004_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-208_S28_L004_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-208_S28_L004_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-208_S28_L004_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-208_S28_L004_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-208_S28_L004_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-208_S28_L004_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-208_S28_L004_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-208_S28_L004_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-208_S28_L004_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-208_S28_L004_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-208_S28_L004_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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-208_S28_L004_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_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: 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Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8641341 lines in total Total number of methylation call strings processed: 17282682 Final Cytosine Methylation Report ================================= Total number of C's analysed: 158634154 Total methylated C's in CpG context: 6281105 Total methylated C's in CHG context: 854946 Total methylated C's in CHH context: 1753269 Total C to T conversions in CpG context: 16254051 Total C to T conversions in CHG context: 33112776 Total C to T conversions in CHH context: 100378007 C methylated in CpG context: 27.9% C methylated in CHG context: 2.5% C methylated in CHH context: 1.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-208_S28_L004_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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-208_S28_L004_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/sr320/1218/CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-208_S28_L004_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-208_S28_L004_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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-208_S28_L004_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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_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 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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 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: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 8641341 lines in total Total number of methylation call strings processed: 17282682 Final Cytosine Methylation Report ================================= Total number of C's analysed: 158634154 Total methylated C's in CpG context: 6281105 Total methylated C's in CHG context: 854946 Total methylated C's in CHH context: 1753269 Total C to T conversions in CpG context: 16254051 Total C to T conversions in CHG context: 33112776 Total C to T conversions in CHH context: 100378007 C methylated in CpG context: 27.9% C methylated in CHG context: 2.5% C methylated in CHH context: 1.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-209_S29_L004_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-209_S29_L004_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-209_S29_L004_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-209_S29_L004_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-209_S29_L004_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-209_S29_L004_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-209_S29_L004_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-209_S29_L004_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-209_S29_L004_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-209_S29_L004_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-209_S29_L004_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-209_S29_L004_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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-209_S29_L004_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_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: 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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.. 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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8945509 lines in total Total number of methylation call strings processed: 17891018 Final Cytosine Methylation Report ================================= Total number of C's analysed: 181303125 Total methylated C's in CpG context: 8133825 Total methylated C's in CHG context: 907176 Total methylated C's in CHH context: 2249034 Total C to T conversions in CpG context: 17357263 Total C to T conversions in CHG context: 37254559 Total C to T conversions in CHH context: 115401268 C methylated in CpG context: 31.9% 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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-209_S29_L004_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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-209_S29_L004_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/sr320/1218/CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-209_S29_L004_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-209_S29_L004_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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-209_S29_L004_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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-209_S29_L004_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 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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 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: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 8945509 lines in total Total number of methylation call strings processed: 17891018 Final Cytosine Methylation Report ================================= Total number of C's analysed: 181303125 Total methylated C's in CpG context: 8133825 Total methylated C's in CHG context: 907176 Total methylated C's in CHH context: 2249034 Total C to T conversions in CpG context: 17357263 Total C to T conversions in CHG context: 37254559 Total C to T conversions in CHH context: 115401268 C methylated in CpG context: 31.9% 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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-214_S30_L004_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-214_S30_L004_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-214_S30_L004_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-214_S30_L004_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-214_S30_L004_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-214_S30_L004_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-214_S30_L004_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-214_S30_L004_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-214_S30_L004_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-214_S30_L004_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-214_S30_L004_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-214_S30_L004_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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-214_S30_L004_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_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: 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Exiting.. Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8703878 lines in total Total number of methylation call strings processed: 17407756 Final Cytosine Methylation Report ================================= Total number of C's analysed: 181129898 Total methylated C's in CpG context: 7299763 Total methylated C's in CHG context: 895027 Total methylated C's in CHH context: 2311106 Total C to T conversions in CpG context: 17951668 Total C to T conversions in CHG context: 36965157 Total C to T conversions in CHH context: 115707177 C methylated in CpG context: 28.9% C methylated in CHG context: 2.4% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-214_S30_L004_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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-214_S30_L004_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/sr320/1218/CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-214_S30_L004_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-214_S30_L004_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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-214_S30_L004_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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_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 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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 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: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 8703878 lines in total Total number of methylation call strings processed: 17407756 Final Cytosine Methylation Report ================================= Total number of C's analysed: 181129898 Total methylated C's in CpG context: 7299763 Total methylated C's in CHG context: 895027 Total methylated C's in CHH context: 2311106 Total C to T conversions in CpG context: 17951668 Total C to T conversions in CHG context: 36965157 Total C to T conversions in CHH context: 115707177 C methylated in CpG context: 28.9% C methylated in CHG context: 2.4% C methylated in CHH context: 2.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-215_S31_L004_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-215_S31_L004_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-215_S31_L004_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-215_S31_L004_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-215_S31_L004_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-215_S31_L004_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-215_S31_L004_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-215_S31_L004_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-215_S31_L004_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-215_S31_L004_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-215_S31_L004_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-215_S31_L004_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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_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: 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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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6392902 lines in total Total number of methylation call strings processed: 12785804 Final Cytosine Methylation Report ================================= Total number of C's analysed: 126318223 Total methylated C's in CpG context: 5908942 Total methylated C's in CHG context: 702435 Total methylated C's in CHH context: 1841804 Total C to T conversions in CpG context: 11618123 Total C to T conversions in CHG context: 25937403 Total C to T conversions in CHH context: 80309516 C methylated in CpG context: 33.7% 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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-215_S31_L004_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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-215_S31_L004_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/sr320/1218/CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-215_S31_L004_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-215_S31_L004_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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-215_S31_L004_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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_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 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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6392902 lines in total Total number of methylation call strings processed: 12785804 Final Cytosine Methylation Report ================================= Total number of C's analysed: 126318223 Total methylated C's in CpG context: 5908942 Total methylated C's in CHG context: 702435 Total methylated C's in CHH context: 1841804 Total C to T conversions in CpG context: 11618123 Total C to T conversions in CHG context: 25937403 Total C to T conversions in CHH context: 80309516 C methylated in CpG context: 33.7% 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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-220_S32_L004_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-220_S32_L004_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-220_S32_L004_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-220_S32_L004_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-220_S32_L004_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-220_S32_L004_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-220_S32_L004_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-220_S32_L004_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-220_S32_L004_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-220_S32_L004_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-220_S32_L004_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-220_S32_L004_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-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-220_S32_L004_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4362357 lines in total Total number of methylation call strings processed: 8724714 Final Cytosine Methylation Report ================================= Total number of C's analysed: 89710026 Total methylated C's in CpG context: 3860035 Total methylated C's in CHG context: 483168 Total methylated C's in CHH context: 1807632 Total C to T conversions in CpG context: 8426280 Total C to T conversions in CHG context: 18264364 Total C to T conversions in CHH context: 56868547 C methylated in CpG context: 31.4% C methylated in CHG context: 2.6% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-220_S32_L004_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-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-220_S32_L004_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/sr320/1218/CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-220_S32_L004_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-220_S32_L004_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-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-220_S32_L004_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-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_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 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: 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.. 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.. Merging individual splitting reports into overall report: 'EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 4362357 lines in total Total number of methylation call strings processed: 8724714 Final Cytosine Methylation Report ================================= Total number of C's analysed: 89710026 Total methylated C's in CpG context: 3860035 Total methylated C's in CHG context: 483168 Total methylated C's in CHH context: 1807632 Total C to T conversions in CpG context: 8426280 Total C to T conversions in CHG context: 18264364 Total C to T conversions in CHH context: 56868547 C methylated in CpG context: 31.4% C methylated in CHG context: 2.6% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-221_S33_L004_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-221_S33_L004_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-221_S33_L004_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-221_S33_L004_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-221_S33_L004_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-221_S33_L004_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-221_S33_L004_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-221_S33_L004_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-221_S33_L004_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-221_S33_L004_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-221_S33_L004_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-221_S33_L004_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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-221_S33_L004_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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-221_S33_L004_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_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 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 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 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4911622 lines in total Total number of methylation call strings processed: 9823244 Final Cytosine Methylation Report ================================= Total number of C's analysed: 96701418 Total methylated C's in CpG context: 4236787 Total methylated C's in CHG context: 538030 Total methylated C's in CHH context: 1814920 Total C to T conversions in CpG context: 9099073 Total C to T conversions in CHG context: 19735564 Total C to T conversions in CHH context: 61277044 C methylated in CpG context: 31.8% C methylated in CHG context: 2.7% C methylated in CHH context: 2.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-221_S33_L004_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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-221_S33_L004_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/sr320/1218/CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-221_S33_L004_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-221_S33_L004_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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-221_S33_L004_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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_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 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 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 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 4911622 lines in total Total number of methylation call strings processed: 9823244 Final Cytosine Methylation Report ================================= Total number of C's analysed: 96701418 Total methylated C's in CpG context: 4236787 Total methylated C's in CHG context: 538030 Total methylated C's in CHH context: 1814920 Total C to T conversions in CpG context: 9099073 Total C to T conversions in CHG context: 19735564 Total C to T conversions in CHH context: 61277044 C methylated in CpG context: 31.8% C methylated in CHG context: 2.7% C methylated in CHH context: 2.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-226_S34_L004_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-226_S34_L004_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-226_S34_L004_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-226_S34_L004_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-226_S34_L004_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-226_S34_L004_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-226_S34_L004_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-226_S34_L004_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-226_S34_L004_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-226_S34_L004_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-226_S34_L004_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-226_S34_L004_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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-226_S34_L004_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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-226_S34_L004_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_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 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.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 3438115 lines in total Total number of methylation call strings processed: 6876230 Final Cytosine Methylation Report ================================= Total number of C's analysed: 74285747 Total methylated C's in CpG context: 3347989 Total methylated C's in CHG context: 403265 Total methylated C's in CHH context: 1509605 Total C to T conversions in CpG context: 6780487 Total C to T conversions in CHG context: 15120311 Total C to T conversions in CHH context: 47124090 C methylated in CpG context: 33.1% C methylated in CHG context: 2.6% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-226_S34_L004_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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-226_S34_L004_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/sr320/1218/CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-226_S34_L004_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-226_S34_L004_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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-226_S34_L004_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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-226_S34_L004_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 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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 3438115 lines in total Total number of methylation call strings processed: 6876230 Final Cytosine Methylation Report ================================= Total number of C's analysed: 74285747 Total methylated C's in CpG context: 3347989 Total methylated C's in CHG context: 403265 Total methylated C's in CHH context: 1509605 Total C to T conversions in CpG context: 6780487 Total C to T conversions in CHG context: 15120311 Total C to T conversions in CHH context: 47124090 C methylated in CpG context: 33.1% C methylated in CHG context: 2.6% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-227_S35_L004_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-227_S35_L004_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-227_S35_L004_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-227_S35_L004_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-227_S35_L004_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-227_S35_L004_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-227_S35_L004_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-227_S35_L004_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-227_S35_L004_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-227_S35_L004_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-227_S35_L004_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-227_S35_L004_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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-227_S35_L004_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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-227_S35_L004_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4209352 lines in total Total number of methylation call strings processed: 8418704 Final Cytosine Methylation Report ================================= Total number of C's analysed: 86316145 Total methylated C's in CpG context: 3751343 Total methylated C's in CHG context: 464615 Total methylated C's in CHH context: 1765502 Total C to T conversions in CpG context: 8102850 Total C to T conversions in CHG context: 17545411 Total C to T conversions in CHH context: 54686424 C methylated in CpG context: 31.6% C methylated in CHG context: 2.6% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-227_S35_L004_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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-227_S35_L004_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/sr320/1218/CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-227_S35_L004_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-227_S35_L004_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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-227_S35_L004_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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 4209352 lines in total Total number of methylation call strings processed: 8418704 Final Cytosine Methylation Report ================================= Total number of C's analysed: 86316145 Total methylated C's in CpG context: 3751343 Total methylated C's in CHG context: 464615 Total methylated C's in CHH context: 1765502 Total C to T conversions in CpG context: 8102850 Total C to T conversions in CHG context: 17545411 Total C to T conversions in CHH context: 54686424 C methylated in CpG context: 31.6% C methylated in CHG context: 2.6% C methylated in CHH context: 3.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-229_S36_L004_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-229_S36_L004_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-229_S36_L004_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-229_S36_L004_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-229_S36_L004_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-229_S36_L004_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-229_S36_L004_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-229_S36_L004_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-229_S36_L004_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-229_S36_L004_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-229_S36_L004_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-229_S36_L004_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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-229_S36_L004_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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-229_S36_L004_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_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 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 Finished processing child process. Exiting.. Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6036266 lines in total Total number of methylation call strings processed: 12072532 Final Cytosine Methylation Report ================================= Total number of C's analysed: 120448317 Total methylated C's in CpG context: 5162434 Total methylated C's in CHG context: 610621 Total methylated C's in CHH context: 1841547 Total C to T conversions in CpG context: 11661347 Total C to T conversions in CHG context: 24880747 Total C to T conversions in CHH context: 76291621 C methylated in CpG context: 30.7% C methylated in CHG context: 2.4% C methylated in CHH context: 2.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-229_S36_L004_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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-229_S36_L004_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/sr320/1218/CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-229_S36_L004_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-229_S36_L004_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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-229_S36_L004_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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_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 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 Finished processing child process. Exiting.. Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 6000000 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: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6036266 lines in total Total number of methylation call strings processed: 12072532 Final Cytosine Methylation Report ================================= Total number of C's analysed: 120448317 Total methylated C's in CpG context: 5162434 Total methylated C's in CHG context: 610621 Total methylated C's in CHH context: 1841547 Total C to T conversions in CpG context: 11661347 Total C to T conversions in CHG context: 24880747 Total C to T conversions in CHH context: 76291621 C methylated in CpG context: 30.7% C methylated in CHG context: 2.4% C methylated in CHH context: 2.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-230_S37_L004_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-230_S37_L004_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-230_S37_L004_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-230_S37_L004_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-230_S37_L004_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-230_S37_L004_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-230_S37_L004_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-230_S37_L004_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-230_S37_L004_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-230_S37_L004_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-230_S37_L004_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-230_S37_L004_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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_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: 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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 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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 7282444 lines in total Total number of methylation call strings processed: 14564888 Final Cytosine Methylation Report ================================= Total number of C's analysed: 139950493 Total methylated C's in CpG context: 5977998 Total methylated C's in CHG context: 651184 Total methylated C's in CHH context: 1768421 Total C to T conversions in CpG context: 13704103 Total C to T conversions in CHG context: 28593233 Total C to T conversions in CHH context: 89255554 C methylated in CpG context: 30.4% C methylated in CHG context: 2.2% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-230_S37_L004_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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-230_S37_L004_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/sr320/1218/CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-230_S37_L004_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-230_S37_L004_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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-230_S37_L004_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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_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: 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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 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.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 7282444 lines in total Total number of methylation call strings processed: 14564888 Final Cytosine Methylation Report ================================= Total number of C's analysed: 139950493 Total methylated C's in CpG context: 5977998 Total methylated C's in CHG context: 651184 Total methylated C's in CHH context: 1768421 Total C to T conversions in CpG context: 13704103 Total C to T conversions in CHG context: 28593233 Total C to T conversions in CHH context: 89255554 C methylated in CpG context: 30.4% C methylated in CHG context: 2.2% C methylated in CHH context: 1.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.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-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 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 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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6399320 lines in total Total number of methylation call strings processed: 12798640 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128539262 Total methylated C's in CpG context: 5867583 Total methylated C's in CHG context: 687621 Total methylated C's in CHH context: 2454676 Total C to T conversions in CpG context: 11862497 Total C to T conversions in CHG context: 26124666 Total C to T conversions in CHH context: 81542219 C methylated in CpG context: 33.1% C methylated in CHG context: 2.6% C methylated in CHH context: 2.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 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 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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6399320 lines in total Total number of methylation call strings processed: 12798640 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128539262 Total methylated C's in CpG context: 5867583 Total methylated C's in CHG context: 687621 Total methylated C's in CHH context: 2454676 Total C to T conversions in CpG context: 11862497 Total C to T conversions in CHG context: 26124666 Total C to T conversions in CHH context: 81542219 C methylated in CpG context: 33.1% C methylated in CHG context: 2.6% C methylated in CHH context: 2.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 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: 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Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8576017 lines in total Total number of methylation call strings processed: 17152034 Final Cytosine Methylation Report ================================= Total number of C's analysed: 167743909 Total methylated C's in CpG context: 8085260 Total methylated C's in CHG context: 910439 Total methylated C's in CHH context: 2251034 Total C to T conversions in CpG context: 15228220 Total C to T conversions in CHG context: 34537608 Total C to T conversions in CHH context: 106731348 C methylated in CpG context: 34.7% C methylated in CHG context: 2.6% C methylated in CHH context: 2.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 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Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 8576017 lines in total Total number of methylation call strings processed: 17152034 Final Cytosine Methylation Report ================================= Total number of C's analysed: 167743909 Total methylated C's in CpG context: 8085260 Total methylated C's in CHG context: 910439 Total methylated C's in CHH context: 2251034 Total C to T conversions in CpG context: 15228220 Total C to T conversions in CHG context: 34537608 Total C to T conversions in CHH context: 106731348 C methylated in CpG context: 34.7% C methylated in CHG context: 2.6% C methylated in CHH context: 2.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 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: 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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.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 6420611 lines in total Total number of methylation call strings processed: 12841222 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128026299 Total methylated C's in CpG context: 5689722 Total methylated C's in CHG context: 671794 Total methylated C's in CHH context: 2537937 Total C to T conversions in CpG context: 11970270 Total C to T conversions in CHG context: 25906277 Total C to T conversions in CHH context: 81250299 C methylated in CpG context: 32.2% C methylated in CHG context: 2.5% C methylated in CHH context: 3.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 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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 Processed lines: 6000000 Processed lines: 6000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 6420611 lines in total Total number of methylation call strings processed: 12841222 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128026299 Total methylated C's in CpG context: 5689722 Total methylated C's in CHG context: 671794 Total methylated C's in CHH context: 2537937 Total C to T conversions in CpG context: 11970270 Total C to T conversions in CHG context: 25906277 Total C to T conversions in CHH context: 81250299 C methylated in CpG context: 32.2% C methylated in CHG context: 2.5% C methylated in CHH context: 3.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Processed lines: 4000000 Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4031044 lines in total Total number of methylation call strings processed: 8062088 Final Cytosine Methylation Report ================================= Total number of C's analysed: 79983322 Total methylated C's in CpG context: 3855731 Total methylated C's in CHG context: 431899 Total methylated C's in CHH context: 1321843 Total C to T conversions in CpG context: 7250942 Total C to T conversions in CHG context: 16319796 Total C to T conversions in CHH context: 50803111 C methylated in CpG context: 34.7% C methylated in CHG context: 2.6% C methylated in CHH context: 2.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1218/CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bam Now reading in Bismark result file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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:Scaffold_01 LN:89643857 skipping SAM header line: @SQ SN:Scaffold_02 LN:69596280 skipping SAM header line: @SQ SN:Scaffold_03 LN:57743597 skipping SAM header line: @SQ SN:Scaffold_04 LN:65288255 skipping SAM header line: @SQ SN:Scaffold_05 LN:67248332 skipping SAM header line: @SQ SN:Scaffold_06 LN:61759565 skipping SAM header line: @SQ SN:Scaffold_07 LN:43120122 skipping SAM header line: @SQ SN:Scaffold_08 LN:61151155 skipping SAM header line: @SQ SN:Scaffold_09 LN:38581958 skipping SAM header line: @SQ SN:Scaffold_10 LN:53961475 skipping SAM header line: @SQ SN:Scaffold_11 LN:51449921 skipping SAM header line: @SQ SN:Scaffold_12 LN:50438331 skipping SAM header line: @SQ SN:Scaffold_13 LN:44396874 skipping SAM header line: @SQ SN:Scaffold_14 LN:45393038 skipping SAM header line: @SQ SN:Scaffold_15 LN:47938513 skipping SAM header line: @SQ SN:Scaffold_16 LN:31980953 skipping SAM header line: @SQ SN:Scaffold_17 LN:34923512 skipping SAM header line: @SQ SN:Scaffold_18 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/v01/ -p 4 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R2_001_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 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.. 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.. Processed lines: 4000000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt' Merging from these individual files: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14 Processed 4031044 lines in total Total number of methylation call strings processed: 8062088 Final Cytosine Methylation Report ================================= Total number of C's analysed: 79983322 Total methylated C's in CpG context: 3855731 Total methylated C's in CHG context: 431899 Total methylated C's in CHH context: 1321843 Total C to T conversions in CpG context: 7250942 Total C to T conversions in CHG context: 16319796 Total C to T conversions in CHH context: 50803111 C methylated in CpG context: 34.7% C methylated in CHG context: 2.6% C methylated in CHH context: 2.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.1.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.2.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.3.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.4.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.5.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.6.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.7.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.8.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.9.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.10.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.11.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.12.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.13.mbias EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CpG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHG_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept CHH_CTOT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt was empty -> deleted CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt CHH_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.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/sr320/1218/CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt /gscratch/scrubbed/sr320/1218/CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt Writing bedGraph to file: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.txt to merged temp file Sorting input file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 52 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Found 2 potential deduplication reports with the same basename (EPI-103_S27_L005_R1_001_val_1_bismark_bt2) in the current directory. Please specify a single report using the option '--dedup_report FILE' or otherwise provide filenames that are easier to figure out... 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 52 Bismark BAM file(s)... >> Reading from Bismark report: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> 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 >> Reading from Bismark report: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... 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Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1218/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-103_S27_L005.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: Scaffold_01 Writing cytosine report for chromosome Scaffold_01 (stored 1084861 different covered positions) Writing cytosine report for chromosome Scaffold_02 (stored 838867 different covered positions) Writing cytosine report for chromosome Scaffold_03 (stored 675348 different covered positions) Writing cytosine report for chromosome Scaffold_04 (stored 771355 different covered positions) Writing cytosine report for chromosome Scaffold_05 (stored 694256 different covered positions) Writing cytosine report for chromosome Scaffold_06 (stored 676942 different covered positions) Writing cytosine report for chromosome Scaffold_07 (stored 495336 different covered positions) Writing cytosine report for chromosome Scaffold_08 (stored 695303 different covered positions) Writing cytosine report for chromosome Scaffold_09 (stored 438486 different covered positions) Writing cytosine report for chromosome Scaffold_10 (stored 575576 different covered positions) Writing cytosine report for chromosome Scaffold_11 (stored 570579 different covered positions) Writing cytosine report for chromosome Scaffold_12 (stored 606443 different covered positions) Writing cytosine report for chromosome Scaffold_13 (stored 489725 different covered positions) Writing cytosine report for chromosome Scaffold_14 (stored 626011 different covered positions) Writing cytosine report for chromosome Scaffold_15 (stored 499547 different covered positions) Writing cytosine report for chromosome Scaffold_16 (stored 395422 different covered positions) Writing cytosine report for chromosome Scaffold_17 (stored 420528 different covered positions) Writing cytosine report for last chromosome Scaffold_18 (stored 304048 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-103_S27_L005.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-103_S27_L005.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1218/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v01/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/ chr Scaffold_01 (89643857 bp) chr Scaffold_02 (69596280 bp) chr Scaffold_03 (57743597 bp) chr Scaffold_04 (65288255 bp) chr Scaffold_05 (67248332 bp) chr Scaffold_06 (61759565 bp) chr Scaffold_07 (43120122 bp) chr Scaffold_08 (61151155 bp) chr Scaffold_09 (38581958 bp) chr Scaffold_10 (53961475 bp) chr Scaffold_11 (51449921 bp) chr Scaffold_12 (50438331 bp) chr Scaffold_13 (44396874 bp) chr Scaffold_14 (45393038 bp) chr Scaffold_15 (47938513 bp) chr Scaffold_16 (31980953 bp) chr Scaffold_17 (34923512 bp) chr Scaffold_18 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz.CpG_report.txt <<< gzip: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.deduplicated.bismark.cov.gz_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz: No such file or directory No last chromosome was defined, something must have gone wrong while reading the data in (e.g. specified wrong file path for a gzipped coverage file?). Please check your command! xargs: /gscratch/srlab/programs/Bismark-0.21.0/coverage2cytosine: exited with status 255; aborting cat: merged_CpG_evidence.cov: No such file or directory