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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH01_06_S1_L001_R1_001_val_1.fq.gz to CH01_06_S1_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH01_06_S1_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH01_06_S1_L001_R2_001_val_2.fq.gz to CH01_06_S1_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH01_06_S1_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH01_06_S1_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_06_S1_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH01_06_S1_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_06_S1_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:3133:1367_1:N:0:NTCACG/1 77 * 0 0 * * 0 0 GGGAGGTTTTTTTAGTTATAGTGTAGTTTTTTATTTGTTTAGTATTTTTAGAGTAGTTTGTAGAGTTTAGGTGTTTAGGGGTTATTTTTATTT FFJFJJ>> Writing bisulfite mapping results to CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 29584 (73.96%) aligned concordantly 0 times 4626 (11.56%) aligned concordantly exactly 1 time 5790 (14.47%) aligned concordantly >1 times 26.04% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 29752 (74.38%) aligned concordantly 0 times 4472 (11.18%) aligned concordantly exactly 1 time 5776 (14.44%) aligned concordantly >1 times 25.62% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH01_06_S1_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_06_S1_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 10749 Mapping efficiency: 26.9% Sequence pairs with no alignments under any condition: 25236 Sequence pairs did not map uniquely: 4015 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: 5277 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5472 ((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: 386106 Total methylated C's in CpG context: 49564 Total methylated C's in CHG context: 1981 Total methylated C's in CHH context: 29190 Total methylated C's in Unknown context: 507 Total unmethylated C's in CpG context: 17256 Total unmethylated C's in CHG context: 78075 Total unmethylated C's in CHH context: 210040 Total unmethylated C's in Unknown context: 1189 C methylated in CpG context: 74.2% C methylated in CHG context: 2.5% C methylated in CHH context: 12.2% C methylated in unknown context (CN or CHN): 29.9% Bismark completed in 0d 0h 0m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH01_14_S2_L001_R1_001_val_1.fq.gz to CH01_14_S2_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH01_14_S2_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH01_14_S2_L001_R2_001_val_2.fq.gz to CH01_14_S2_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH01_14_S2_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH01_14_S2_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_14_S2_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH01_14_S2_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_14_S2_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:2057:1367_1:N:0:NGATGT/1 99 PGA_scaffold12__214_contigs__length_38711105_CT_converted 34830842 1 50M = 34830878 85 GTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT JFF>> Writing bisulfite mapping results to CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 28671 (71.68%) aligned concordantly 0 times 4292 (10.73%) aligned concordantly exactly 1 time 7037 (17.59%) aligned concordantly >1 times 28.32% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 28541 (71.35%) aligned concordantly 0 times 4365 (10.91%) aligned concordantly exactly 1 time 7094 (17.73%) aligned concordantly >1 times 28.65% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH01_14_S2_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_14_S2_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 10453 Mapping efficiency: 26.1% Sequence pairs with no alignments under any condition: 24414 Sequence pairs did not map uniquely: 5133 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: 5227 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5226 ((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: 316126 Total methylated C's in CpG context: 32191 Total methylated C's in CHG context: 1533 Total methylated C's in CHH context: 31987 Total methylated C's in Unknown context: 434 Total unmethylated C's in CpG context: 15010 Total unmethylated C's in CHG context: 57875 Total unmethylated C's in CHH context: 177530 Total unmethylated C's in Unknown context: 1251 C methylated in CpG context: 68.2% C methylated in CHG context: 2.6% C methylated in CHH context: 15.3% C methylated in unknown context (CN or CHN): 25.8% Bismark completed in 0d 0h 0m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH01_22_S3_L001_R1_001_val_1.fq.gz to CH01_22_S3_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH01_22_S3_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH01_22_S3_L001_R2_001_val_2.fq.gz to CH01_22_S3_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH01_22_S3_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH01_22_S3_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_22_S3_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH01_22_S3_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_22_S3_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:4777:1367_1:N:0:NTAGGC/1 77 * 0 0 * * 0 0 ATTTTTTAATATGTTTTAATTAAATTGTTATAATTTTTATATTTTTATTAAAATAAAAAATTTTTTTTTTATAGTTTTATAATAATTTAAATTATATTATTAGATTGAAAATTATAAATTAAATATTATT JJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJ YT:Z:UP K00337:412:HKTCJBBXY:1:1101:4777:1367_2:N:0:NTAGGC/2 141 * 0 0 * * 0 0 CCAATTTATTATTATAAATTATTAAATTAATTTATATATAATTAAAAATATTTTATTATCTATAAATAATTTTAATAATAAAAAATTTTTAATATATAATTTTCAATCAAATAATATATTTTAAATTA JJFJJFAAFFAJ>> Writing bisulfite mapping results to CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 29130 (72.83%) aligned concordantly 0 times 4589 (11.47%) aligned concordantly exactly 1 time 6281 (15.70%) aligned concordantly >1 times 27.18% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 29079 (72.70%) aligned concordantly 0 times 4700 (11.75%) aligned concordantly exactly 1 time 6221 (15.55%) aligned concordantly >1 times 27.30% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH01_22_S3_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_22_S3_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 11096 Mapping efficiency: 27.7% Sequence pairs with no alignments under any condition: 24527 Sequence pairs did not map uniquely: 4377 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: 5467 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5629 ((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: 388262 Total methylated C's in CpG context: 39461 Total methylated C's in CHG context: 1899 Total methylated C's in CHH context: 32004 Total methylated C's in Unknown context: 420 Total unmethylated C's in CpG context: 20309 Total unmethylated C's in CHG context: 75430 Total unmethylated C's in CHH context: 219159 Total unmethylated C's in Unknown context: 1240 C methylated in CpG context: 66.0% C methylated in CHG context: 2.5% C methylated in CHH context: 12.7% C methylated in unknown context (CN or CHN): 25.3% Bismark completed in 0d 0h 0m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH01_38_S4_L001_R1_001_val_1.fq.gz to CH01_38_S4_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH01_38_S4_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH01_38_S4_L001_R2_001_val_2.fq.gz to CH01_38_S4_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH01_38_S4_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH01_38_S4_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_38_S4_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH01_38_S4_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_38_S4_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:4066:1367_1:N:0:NGACCA/1 77 * 0 0 * * 0 0 AGGATAAATATTATAGTTAGTTGTGAGGGTAGTTGGAATTGAAGAAGATTTAAAGTGAATTAAATAGGTAAAAAATTTAGGGTTGGTATTAAAAGTAATATTAGTATTAATAGAAATAATTTGATTAG JJJJFFJFJJJJJJJ-->> Writing bisulfite mapping results to CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 28830 (72.08%) aligned concordantly 0 times 4520 (11.30%) aligned concordantly exactly 1 time 6650 (16.62%) aligned concordantly >1 times 27.93% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 28885 (72.21%) aligned concordantly 0 times 4457 (11.14%) aligned concordantly exactly 1 time 6658 (16.64%) aligned concordantly >1 times 27.79% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH01_38_S4_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH01_38_S4_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 10756 Mapping efficiency: 26.9% Sequence pairs with no alignments under any condition: 24552 Sequence pairs did not map uniquely: 4692 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: 5390 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5366 ((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: 332027 Total methylated C's in CpG context: 32931 Total methylated C's in CHG context: 1933 Total methylated C's in CHH context: 36160 Total methylated C's in Unknown context: 586 Total unmethylated C's in CpG context: 15848 Total unmethylated C's in CHG context: 63167 Total unmethylated C's in CHH context: 181988 Total unmethylated C's in Unknown context: 1304 C methylated in CpG context: 67.5% C methylated in CHG context: 3.0% C methylated in CHH context: 16.6% C methylated in unknown context (CN or CHN): 31.0% Bismark completed in 0d 0h 1m 0s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH03_04_S5_L001_R1_001_val_1.fq.gz to CH03_04_S5_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH03_04_S5_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH03_04_S5_L001_R2_001_val_2.fq.gz to CH03_04_S5_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH03_04_S5_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH03_04_S5_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH03_04_S5_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH03_04_S5_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH03_04_S5_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:2889:1367_1:N:0:NCAGTG/1 77 * 0 0 * * 0 0 AAAATATAAATATAAGATTTTTGATATTGTAAGTATATGGAGAGAAAAATGTAAAGGATATTGTTATGGGTTGATGTTGTGTG JJJJJJJJJJJJJJJJJ>> Writing bisulfite mapping results to CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 28249 (70.62%) aligned concordantly 0 times 2888 (7.22%) aligned concordantly exactly 1 time 8863 (22.16%) aligned concordantly >1 times 29.38% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 28262 (70.66%) aligned concordantly 0 times 2892 (7.23%) aligned concordantly exactly 1 time 8846 (22.11%) aligned concordantly >1 times 29.34% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH03_04_S5_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH03_04_S5_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 8170 Mapping efficiency: 20.4% Sequence pairs with no alignments under any condition: 25243 Sequence pairs did not map uniquely: 6587 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: 4112 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4058 ((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: 227949 Total methylated C's in CpG context: 3158 Total methylated C's in CHG context: 1284 Total methylated C's in CHH context: 67053 Total methylated C's in Unknown context: 808 Total unmethylated C's in CpG context: 24230 Total unmethylated C's in CHG context: 30897 Total unmethylated C's in CHH context: 101327 Total unmethylated C's in Unknown context: 1099 C methylated in CpG context: 11.5% C methylated in CHG context: 4.0% C methylated in CHH context: 39.8% C methylated in unknown context (CN or CHN): 42.4% Bismark completed in 0d 0h 0m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH03_15_S6_L001_R1_001_val_1.fq.gz to CH03_15_S6_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH03_15_S6_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH03_15_S6_L001_R2_001_val_2.fq.gz to CH03_15_S6_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH03_15_S6_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH03_15_S6_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH03_15_S6_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH03_15_S6_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH03_15_S6_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:1895:1367_1:N:0:NCCAAT/1 77 * 0 0 * * 0 0 ATTTAAATAATTAATTAAAATAAAATATATTTTTTATATTT JFJJJJJJJJJJJJJ>> Writing bisulfite mapping results to CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 30903 (77.26%) aligned concordantly 0 times 3169 (7.92%) aligned concordantly exactly 1 time 5928 (14.82%) aligned concordantly >1 times 22.74% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 31032 (77.58%) aligned concordantly 0 times 3012 (7.53%) aligned concordantly exactly 1 time 5956 (14.89%) aligned concordantly >1 times 22.42% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH03_15_S6_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH03_15_S6_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 7805 Mapping efficiency: 19.5% Sequence pairs with no alignments under any condition: 27769 Sequence pairs did not map uniquely: 4426 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: 3810 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3995 ((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: 253302 Total methylated C's in CpG context: 6843 Total methylated C's in CHG context: 1218 Total methylated C's in CHH context: 39938 Total methylated C's in Unknown context: 441 Total unmethylated C's in CpG context: 27922 Total unmethylated C's in CHG context: 41596 Total unmethylated C's in CHH context: 135785 Total unmethylated C's in Unknown context: 1079 C methylated in CpG context: 19.7% C methylated in CHG context: 2.8% C methylated in CHH context: 22.7% C methylated in unknown context (CN or CHN): 29.0% Bismark completed in 0d 0h 0m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH03_33_S7_L001_R1_001_val_1.fq.gz to CH03_33_S7_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH03_33_S7_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH03_33_S7_L001_R2_001_val_2.fq.gz to CH03_33_S7_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH03_33_S7_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH03_33_S7_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH03_33_S7_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH03_33_S7_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH03_33_S7_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:1874:1367_1:N:0:NAGATC/1 77 * 0 0 * * 0 0 TATTATAAATTTTAAATTTTTTTTATAAAAAAATGATTGATTATTTTGAAAAAAATTAATAATAATAAATTATATAATAAATTATATATATAAAATTATATTAATTAATTTTATATAATTTTTTTAT JJJJJJJJJJJJJJJJ7-F7AFFAJFJJJJJJJFJJJFJJFJJAJAFFAJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJAJFFFJJJJJJJJJJ>> Writing bisulfite mapping results to CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 30405 (76.01%) aligned concordantly 0 times 4443 (11.11%) aligned concordantly exactly 1 time 5152 (12.88%) aligned concordantly >1 times 23.99% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 30306 (75.77%) aligned concordantly 0 times 4546 (11.37%) aligned concordantly exactly 1 time 5148 (12.87%) aligned concordantly >1 times 24.23% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH03_33_S7_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH03_33_S7_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 10579 Mapping efficiency: 26.4% Sequence pairs with no alignments under any condition: 26007 Sequence pairs did not map uniquely: 3414 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: 5210 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5369 ((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: 405282 Total methylated C's in CpG context: 50005 Total methylated C's in CHG context: 2008 Total methylated C's in CHH context: 28307 Total methylated C's in Unknown context: 457 Total unmethylated C's in CpG context: 18391 Total unmethylated C's in CHG context: 82640 Total unmethylated C's in CHH context: 223931 Total unmethylated C's in Unknown context: 1064 C methylated in CpG context: 73.1% C methylated in CHG context: 2.4% C methylated in CHH context: 11.2% C methylated in unknown context (CN or CHN): 30.0% Bismark completed in 0d 0h 0m 53s ==================== 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH05_01_S8_L001_R1_001_val_1.fq.gz to CH05_01_S8_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH05_01_S8_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH05_01_S8_L001_R2_001_val_2.fq.gz to CH05_01_S8_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH05_01_S8_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH05_01_S8_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_01_S8_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH05_01_S8_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_01_S8_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:3742:1367_1:N:0:NCTTGA/1 77 * 0 0 * * 0 0 TTTTTGATTTATTTAGTTTTGGTGAGGATGGTGTTATGGTAGTAAGTGGGTGTTTTTATTTGGAAAGGATTTAGAGGATAGTTATAAGAATGGTATTGGAATTGAAGG JJFJJJJJJJJJJJJA->> Writing bisulfite mapping results to CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 27593 (68.98%) aligned concordantly 0 times 3541 (8.85%) aligned concordantly exactly 1 time 8866 (22.16%) aligned concordantly >1 times 31.02% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 27589 (68.97%) aligned concordantly 0 times 3684 (9.21%) aligned concordantly exactly 1 time 8727 (21.82%) aligned concordantly >1 times 31.03% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH05_01_S8_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_01_S8_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 9690 Mapping efficiency: 24.2% Sequence pairs with no alignments under any condition: 23982 Sequence pairs did not map uniquely: 6328 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: 4866 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4824 ((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: 274902 Total methylated C's in CpG context: 17640 Total methylated C's in CHG context: 1653 Total methylated C's in CHH context: 58502 Total methylated C's in Unknown context: 704 Total unmethylated C's in CpG context: 16961 Total unmethylated C's in CHG context: 46121 Total unmethylated C's in CHH context: 134025 Total unmethylated C's in Unknown context: 1148 C methylated in CpG context: 51.0% C methylated in CHG context: 3.5% C methylated in CHH context: 30.4% C methylated in unknown context (CN or CHN): 38.0% Bismark completed in 0d 0h 1m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH05_06_S9_L001_R1_001_val_1.fq.gz to CH05_06_S9_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH05_06_S9_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH05_06_S9_L001_R2_001_val_2.fq.gz to CH05_06_S9_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH05_06_S9_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH05_06_S9_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_06_S9_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH05_06_S9_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_06_S9_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:4513:1367_1:N:0:NATCAG/1 99 PGA_scaffold23__65_contigs__length_9586800_CT_converted 9236777 1 83M = 9236777 -83 TGTGTTTATTGGTATTTGTTATATATTATAAGGATTGGAAAATTTTGTAGATTTTGAATTTATGTTTGAAAATTTAATATGAG JJFJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJ AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:83 YS:i:0 YT:Z:CP K00337:412:HKTCJBBXY:1:1101:4513:1367_2:N:0:NATCAG/2 147 PGA_scaffold23__65_contigs__length_9586800_CT_converted 9236777 1 83M = 9236777 -83 TGTGTTTATTGGTATTTGTTATATATTATAAGGATTGGAAAATTTTGTAGATTTTGAATTTATGTTTGAAAATTTAATATGAG JJFJJJJFJJJJJJJJFJJJJJJJFJJJAFAJJJJFJF>> Writing bisulfite mapping results to CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 31562 (78.91%) aligned concordantly 0 times 2916 (7.29%) aligned concordantly exactly 1 time 5522 (13.80%) aligned concordantly >1 times 21.09% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 31506 (78.77%) aligned concordantly 0 times 2954 (7.38%) aligned concordantly exactly 1 time 5540 (13.85%) aligned concordantly >1 times 21.23% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH05_06_S9_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_06_S9_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 7446 Mapping efficiency: 18.6% Sequence pairs with no alignments under any condition: 28479 Sequence pairs did not map uniquely: 4075 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: 3706 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3740 ((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: 266383 Total methylated C's in CpG context: 2503 Total methylated C's in CHG context: 886 Total methylated C's in CHH context: 30953 Total methylated C's in Unknown context: 419 Total unmethylated C's in CpG context: 32087 Total unmethylated C's in CHG context: 43557 Total unmethylated C's in CHH context: 156397 Total unmethylated C's in Unknown context: 950 C methylated in CpG context: 7.2% C methylated in CHG context: 2.0% C methylated in CHH context: 16.5% C methylated in unknown context (CN or CHN): 30.6% Bismark completed in 0d 0h 0m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH05_21_S10_L001_R1_001_val_1.fq.gz to CH05_21_S10_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH05_21_S10_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH05_21_S10_L001_R2_001_val_2.fq.gz to CH05_21_S10_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH05_21_S10_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH05_21_S10_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_21_S10_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH05_21_S10_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_21_S10_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:4980:1367_1:N:0:NAGCTT/1 77 * 0 0 * * 0 0 TTTTTGGGGTGGGGATTTTGATTATGTAGTTTGTATTTGTTATTAAGAAATGGGGATATTGTGTTAATGGGTTGA JJJJJJJJJJJJJJJJ>> Writing bisulfite mapping results to CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 28808 (72.02%) aligned concordantly 0 times 4599 (11.50%) aligned concordantly exactly 1 time 6593 (16.48%) aligned concordantly >1 times 27.98% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 29055 (72.64%) aligned concordantly 0 times 4400 (11.00%) aligned concordantly exactly 1 time 6545 (16.36%) aligned concordantly >1 times 27.36% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH05_21_S10_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_21_S10_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 11042 Mapping efficiency: 27.6% Sequence pairs with no alignments under any condition: 24534 Sequence pairs did not map uniquely: 4424 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: 5664 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5378 ((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: 377848 Total methylated C's in CpG context: 33632 Total methylated C's in CHG context: 2174 Total methylated C's in CHH context: 50208 Total methylated C's in Unknown context: 605 Total unmethylated C's in CpG context: 19353 Total unmethylated C's in CHG context: 71127 Total unmethylated C's in CHH context: 201354 Total unmethylated C's in Unknown context: 1326 C methylated in CpG context: 63.5% C methylated in CHG context: 3.0% C methylated in CHH context: 20.0% C methylated in unknown context (CN or CHN): 31.3% Bismark completed in 0d 0h 1m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH05_24_S11_L001_R1_001_val_1.fq.gz to CH05_24_S11_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH05_24_S11_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH05_24_S11_L001_R2_001_val_2.fq.gz to CH05_24_S11_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH05_24_S11_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH05_24_S11_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_24_S11_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH05_24_S11_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_24_S11_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:2483:1367_1:N:0:NGCTAC/1 99 PGA_scaffold43__161_contigs__length_26349757_CT_converted 22213893 8 103M = 22213873 -123 TTTTTTATTTAAAAATTTTGGGATTAAGATATTTTTTGGATTTTAGAATTAAATATTTTTAGTGTAGATTTTTTAGTGTAGATTTTAATGTTTTTTAAATAAA JJJJJJJJJJJJJJJJ-7JJJJJJJJJJJJJJJJJJJFJJJJFJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:103 YS:i:-76 YT:Z:CP K00337:412:HKTCJBBXY:1:1101:2483:1367_2:N:0:NGCTAC/2 147 PGA_scaffold43__161_contigs__length_26349757_CT_converted 22213873 8 15M3I3M3I105M = 22213893 123 GTTTTTTTTTTGGTTTGGGTTGTAAATTTTTTATTTAATAATTTTGGGATTAAGATATTTTTTGGATTTTAGAATTAAATATTTTTAGTGTAGATTTTTTAGTGTAGATTTTAATGTTTTTTAAATAAA 7---77-<7-A7-7-AJJFF-7---7AFJFFF-F>> Writing bisulfite mapping results to CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 27754 (69.39%) aligned concordantly 0 times 4689 (11.72%) aligned concordantly exactly 1 time 7557 (18.89%) aligned concordantly >1 times 30.61% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 27766 (69.42%) aligned concordantly 0 times 4724 (11.81%) aligned concordantly exactly 1 time 7510 (18.77%) aligned concordantly >1 times 30.59% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH05_24_S11_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH05_24_S11_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 11605 Mapping efficiency: 29.0% Sequence pairs with no alignments under any condition: 23146 Sequence pairs did not map uniquely: 5249 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: 5827 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5778 ((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: 358840 Total methylated C's in CpG context: 42344 Total methylated C's in CHG context: 2457 Total methylated C's in CHH context: 45257 Total methylated C's in Unknown context: 598 Total unmethylated C's in CpG context: 16609 Total unmethylated C's in CHG context: 71351 Total unmethylated C's in CHH context: 180822 Total unmethylated C's in Unknown context: 1200 C methylated in CpG context: 71.8% C methylated in CHG context: 3.3% C methylated in CHH context: 20.0% C methylated in unknown context (CN or CHN): 33.3% Bismark completed in 0d 0h 0m 59s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH07_06_S12_L001_R1_001_val_1.fq.gz to CH07_06_S12_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH07_06_S12_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH07_06_S12_L001_R2_001_val_2.fq.gz to CH07_06_S12_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH07_06_S12_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH07_06_S12_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH07_06_S12_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH07_06_S12_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH07_06_S12_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:2686:1367_1:N:0:NGTCAA/1 77 * 0 0 * * 0 0 ATTTTGATTATTTAATATTTAATATTTTTATTATTTAATTATTTATAAATAATAATAATTTAAAAAT JJJJJJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJFJFJJFFJJ>> Writing bisulfite mapping results to CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 29638 (74.09%) aligned concordantly 0 times 4391 (10.98%) aligned concordantly exactly 1 time 5971 (14.93%) aligned concordantly >1 times 25.91% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 29643 (74.11%) aligned concordantly 0 times 4395 (10.99%) aligned concordantly exactly 1 time 5962 (14.90%) aligned concordantly >1 times 25.89% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH07_06_S12_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH07_06_S12_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 10586 Mapping efficiency: 26.5% Sequence pairs with no alignments under any condition: 25357 Sequence pairs did not map uniquely: 4057 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: 5296 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5290 ((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: 371313 Total methylated C's in CpG context: 38338 Total methylated C's in CHG context: 2126 Total methylated C's in CHH context: 39318 Total methylated C's in Unknown context: 603 Total unmethylated C's in CpG context: 20787 Total unmethylated C's in CHG context: 70417 Total unmethylated C's in CHH context: 200327 Total unmethylated C's in Unknown context: 1264 C methylated in CpG context: 64.8% C methylated in CHG context: 2.9% C methylated in CHH context: 16.4% C methylated in unknown context (CN or CHN): 32.3% Bismark completed in 0d 0h 0m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH07_11_S13_L001_R1_001_val_1.fq.gz to CH07_11_S13_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH07_11_S13_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH07_11_S13_L001_R2_001_val_2.fq.gz to CH07_11_S13_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH07_11_S13_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH07_11_S13_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH07_11_S13_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH07_11_S13_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH07_11_S13_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:1773:1367_1:N:0:NGTTCC/1 77 * 0 0 * * 0 0 GTTGGTGGATTTTTAGTTTGTATTTGTTG JJJJJJJJJJJJJJJFAAJJJJJJJJJJJ YT:Z:UP K00337:412:HKTCJBBXY:1:1101:1773:1367_2:N:0:NGTTCC/2 141 * 0 0 * * 0 0 CAACTAATACAAACTAAAAATCCACCAAC JJ7F-FF>> Writing bisulfite mapping results to CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 31699 (79.25%) aligned concordantly 0 times 2987 (7.47%) aligned concordantly exactly 1 time 5314 (13.29%) aligned concordantly >1 times 20.75% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 31631 (79.08%) aligned concordantly 0 times 3040 (7.60%) aligned concordantly exactly 1 time 5329 (13.32%) aligned concordantly >1 times 20.92% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH07_11_S13_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH07_11_S13_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 7454 Mapping efficiency: 18.6% Sequence pairs with no alignments under any condition: 28610 Sequence pairs did not map uniquely: 3936 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: 3797 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3657 ((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: 257188 Total methylated C's in CpG context: 2676 Total methylated C's in CHG context: 1367 Total methylated C's in CHH context: 31793 Total methylated C's in Unknown context: 485 Total unmethylated C's in CpG context: 29922 Total unmethylated C's in CHG context: 42578 Total unmethylated C's in CHH context: 148852 Total unmethylated C's in Unknown context: 983 C methylated in CpG context: 8.2% C methylated in CHG context: 3.1% C methylated in CHH context: 17.6% C methylated in unknown context (CN or CHN): 33.0% Bismark completed in 0d 0h 1m 0s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH07_24_S14_L001_R1_001_val_1.fq.gz to CH07_24_S14_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH07_24_S14_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH07_24_S14_L001_R2_001_val_2.fq.gz to CH07_24_S14_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH07_24_S14_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH07_24_S14_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH07_24_S14_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH07_24_S14_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH07_24_S14_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:3681:1367_1:N:0:NTGTCA/1 99 PGA_scaffold35__36_contigs__length_7416912_CT_converted 3216683 1 59M = 3216683 -59 GTTAGGTTAGGTTAGGTAAGGTTAGGTAAGGTTAGGTTAGGTTATGTAAGGTTAGGTTA JFFJJJFJJJJFJJJFFFJJJFJJJJFFJJJJJJJJFAJJJJFJJFJJJJJFJJJJFJJ AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:44G14 YS:i:-12 YT:Z:CP K00337:412:HKTCJBBXY:1:1101:3681:1367_2:N:0:NTGTCA/2 147 PGA_scaffold35__36_contigs__length_7416912_CT_converted 3216683 1 59M = 3216683 -59 GTTAGGTTAGGTTAGGTAAGGTTAGGTAAGGTTAGGTTAGGTTATGTGAGGTTAGGTTA JJF7JJFJAFJJA-FJA7-JJA-AJJ<--JJJJJJJJFAJJJJFFJ<-FJJFF>> Writing bisulfite mapping results to CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 29726 (74.31%) aligned concordantly 0 times 3408 (8.52%) aligned concordantly exactly 1 time 6866 (17.16%) aligned concordantly >1 times 25.68% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 29701 (74.25%) aligned concordantly 0 times 3503 (8.76%) aligned concordantly exactly 1 time 6796 (16.99%) aligned concordantly >1 times 25.75% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH07_24_S14_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH07_24_S14_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 8520 Mapping efficiency: 21.3% Sequence pairs with no alignments under any condition: 26290 Sequence pairs did not map uniquely: 5190 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: 4281 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4239 ((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: 285564 Total methylated C's in CpG context: 2441 Total methylated C's in CHG context: 1116 Total methylated C's in CHH context: 34424 Total methylated C's in Unknown context: 547 Total unmethylated C's in CpG context: 31542 Total unmethylated C's in CHG context: 42341 Total unmethylated C's in CHH context: 173700 Total unmethylated C's in Unknown context: 1324 C methylated in CpG context: 7.2% C methylated in CHG context: 2.6% C methylated in CHH context: 16.5% C methylated in unknown context (CN or CHN): 29.2% Bismark completed in 0d 0h 0m 59s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH09_02_S15_L001_R1_001_val_1.fq.gz to CH09_02_S15_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH09_02_S15_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH09_02_S15_L001_R2_001_val_2.fq.gz to CH09_02_S15_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH09_02_S15_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH09_02_S15_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH09_02_S15_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH09_02_S15_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH09_02_S15_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:2341:1367_1:N:0:NCGTCC/1 77 * 0 0 * * 0 0 TTTATAATGTATAGTTTTAGGAATTTTGGTTAAAATTTTAATGGGTGGTAAATGTGAAAAATTTGTAATGTTTTTTTTTGTTTGATTTTAATTTTTTGATATTTATTTTTTTGATTATAGATGTTGTATTT JJJJJJJJJJJJJJJJ-JFJJJJJJJJJJJJJJJJJJFJJJJFJJJJFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJ YT:Z:UP K00337:412:HKTCJBBXY:1:1101:2341:1367_2:N:0:NCGTCC/2 141 * 0 0 * * 0 0 CAACATCAACAAAACAAACATCTAAAAAAACCACAAAAAAAAATATAAAAAAAATACAACATCTATAAACAAAAAAATAAATATCAAAAAAATAAAAACAAACAAAAAAAAACATTACAAAAAAAACACA JJJF7-->> Writing bisulfite mapping results to CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 27716 (69.29%) aligned concordantly 0 times 4516 (11.29%) aligned concordantly exactly 1 time 7768 (19.42%) aligned concordantly >1 times 30.71% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 27759 (69.40%) aligned concordantly 0 times 4510 (11.28%) aligned concordantly exactly 1 time 7731 (19.33%) aligned concordantly >1 times 30.60% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH09_02_S15_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH09_02_S15_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 11144 Mapping efficiency: 27.9% Sequence pairs with no alignments under any condition: 23373 Sequence pairs did not map uniquely: 5483 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: 5489 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5655 ((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: 332075 Total methylated C's in CpG context: 33312 Total methylated C's in CHG context: 2204 Total methylated C's in CHH context: 47777 Total methylated C's in Unknown context: 769 Total unmethylated C's in CpG context: 15207 Total unmethylated C's in CHG context: 58730 Total unmethylated C's in CHH context: 174845 Total unmethylated C's in Unknown context: 1375 C methylated in CpG context: 68.7% C methylated in CHG context: 3.6% C methylated in CHH context: 21.5% C methylated in unknown context (CN or CHN): 35.9% Bismark completed in 0d 0h 1m 2s ==================== 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH09_13_S16_L001_R1_001_val_1.fq.gz to CH09_13_S16_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH09_13_S16_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH09_13_S16_L001_R2_001_val_2.fq.gz to CH09_13_S16_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH09_13_S16_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH09_13_S16_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH09_13_S16_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH09_13_S16_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH09_13_S16_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:1813:1367_1:N:0:NTCCGC/1 77 * 0 0 * * 0 0 AAATTAAATAATTTAATTAATTTATTAAAATA JJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJ YT:Z:UP K00337:412:HKTCJBBXY:1:1101:1813:1367_2:N:0:NTCCGC/2 141 * 0 0 * * 0 0 TATTTTAATAAAATAATTAAATTA FF-A-<7<<-FF-<-FFFJF---< YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CH09_13_S16_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH09_13_S16_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:1813:1367_1:N:0:NTCCGC/1 77 * 0 0 * * 0 0 AAATTAAATAATTTAATTAATTTATTAAAATA JJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJ YT:Z:UP K00337:412:HKTCJBBXY:1:1101:1813:1367_2:N:0:NTCCGC/2 141 * 0 0 * * 0 0 TATTTTAATAAAATAATTAAATTA FF-A-<7<<-FF-<-FFFJF---< YT:Z:UP >>> Writing bisulfite mapping results to CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 28101 (70.25%) aligned concordantly 0 times 4742 (11.86%) aligned concordantly exactly 1 time 7157 (17.89%) aligned concordantly >1 times 29.75% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 28070 (70.17%) aligned concordantly 0 times 4652 (11.63%) aligned concordantly exactly 1 time 7278 (18.20%) aligned concordantly >1 times 29.82% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH09_13_S16_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH09_13_S16_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 11691 Mapping efficiency: 29.2% Sequence pairs with no alignments under any condition: 23421 Sequence pairs did not map uniquely: 4888 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: 5843 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5848 ((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: 431064 Total methylated C's in CpG context: 24420 Total methylated C's in CHG context: 2009 Total methylated C's in CHH context: 48147 Total methylated C's in Unknown context: 684 Total unmethylated C's in CpG context: 25606 Total unmethylated C's in CHG context: 71773 Total unmethylated C's in CHH context: 259109 Total unmethylated C's in Unknown context: 1396 C methylated in CpG context: 48.8% C methylated in CHG context: 2.7% C methylated in CHH context: 15.7% C methylated in unknown context (CN or CHN): 32.9% Bismark completed in 0d 0h 0m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH09_28_S17_L001_R1_001_val_1.fq.gz to CH09_28_S17_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH09_28_S17_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH09_28_S17_L001_R2_001_val_2.fq.gz to CH09_28_S17_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH09_28_S17_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH09_28_S17_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH09_28_S17_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH09_28_S17_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH09_28_S17_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:5122:1367_1:N:0:NTGAAA/1 77 * 0 0 * * 0 0 AAATTTGTAAAATTTGATATATTAAATTTTTTTTTTTTTTTTTAATAAATATAA JJJJJJJJJJJJJJJ>> Writing bisulfite mapping results to CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 29933 (74.83%) aligned concordantly 0 times 4614 (11.54%) aligned concordantly exactly 1 time 5453 (13.63%) aligned concordantly >1 times 25.17% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 29910 (74.78%) aligned concordantly 0 times 4643 (11.61%) aligned concordantly exactly 1 time 5447 (13.62%) aligned concordantly >1 times 25.23% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH09_28_S17_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH09_28_S17_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 10849 Mapping efficiency: 27.1% Sequence pairs with no alignments under any condition: 25410 Sequence pairs did not map uniquely: 3741 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: 5416 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5433 ((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: 370094 Total methylated C's in CpG context: 37967 Total methylated C's in CHG context: 2740 Total methylated C's in CHH context: 37987 Total methylated C's in Unknown context: 585 Total unmethylated C's in CpG context: 18254 Total unmethylated C's in CHG context: 72007 Total unmethylated C's in CHH context: 201139 Total unmethylated C's in Unknown context: 1195 C methylated in CpG context: 67.5% C methylated in CHG context: 3.7% C methylated in CHH context: 15.9% C methylated in unknown context (CN or CHN): 32.9% Bismark completed in 0d 0h 0m 55s ==================== 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH10_01_S18_L001_R1_001_val_1.fq.gz to CH10_01_S18_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH10_01_S18_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH10_01_S18_L001_R2_001_val_2.fq.gz to CH10_01_S18_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH10_01_S18_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH10_01_S18_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH10_01_S18_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH10_01_S18_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH10_01_S18_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:2838:1384_1:N:0:NTTTCG/1 77 * 0 0 * * 0 0 ATTAAAAATTTTATTATATAATTTAATAATAAAATTTTTTTAATAA JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJAFJJ-FJ7F YT:Z:UP K00337:412:HKTCJBBXY:1:1101:2838:1384_2:N:0:NTTTCG/2 141 * 0 0 * * 0 0 TTATTAAAAAAATTTTATTATAAAATTATAAAATAAATTTTAAAAT <---<<>> Writing bisulfite mapping results to CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 29122 (72.81%) aligned concordantly 0 times 4709 (11.77%) aligned concordantly exactly 1 time 6169 (15.42%) aligned concordantly >1 times 27.20% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 29110 (72.78%) aligned concordantly 0 times 4656 (11.64%) aligned concordantly exactly 1 time 6234 (15.59%) aligned concordantly >1 times 27.23% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH10_01_S18_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH10_01_S18_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 11202 Mapping efficiency: 28.0% Sequence pairs with no alignments under any condition: 24587 Sequence pairs did not map uniquely: 4211 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: 5634 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5568 ((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: 367157 Total methylated C's in CpG context: 39840 Total methylated C's in CHG context: 2387 Total methylated C's in CHH context: 36274 Total methylated C's in Unknown context: 545 Total unmethylated C's in CpG context: 15927 Total unmethylated C's in CHG context: 71440 Total unmethylated C's in CHH context: 201289 Total unmethylated C's in Unknown context: 1260 C methylated in CpG context: 71.4% C methylated in CHG context: 3.2% C methylated in CHH context: 15.3% C methylated in unknown context (CN or CHN): 30.2% Bismark completed in 0d 0h 0m 59s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH10_08_S19_L001_R1_001_val_1.fq.gz to CH10_08_S19_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH10_08_S19_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH10_08_S19_L001_R2_001_val_2.fq.gz to CH10_08_S19_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH10_08_S19_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH10_08_S19_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH10_08_S19_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH10_08_S19_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH10_08_S19_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:2564:1367_1:N:0:NGTACG/1 77 * 0 0 * * 0 0 GTTATATTATTATGTATATAAAATATAATAATAAAATAATTATATATTTTATATTTAATATTAATTATATATATAATATTTTATTTAATATTTTTTTGAATATTATTGTTTTTTAATATATTTATAAAAAA JJFJJJJJFJJ>> Writing bisulfite mapping results to CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 28768 (71.92%) aligned concordantly 0 times 3469 (8.67%) aligned concordantly exactly 1 time 7763 (19.41%) aligned concordantly >1 times 28.08% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 28631 (71.58%) aligned concordantly 0 times 3534 (8.84%) aligned concordantly exactly 1 time 7835 (19.59%) aligned concordantly >1 times 28.42% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH10_08_S19_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH10_08_S19_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 9279 Mapping efficiency: 23.2% Sequence pairs with no alignments under any condition: 25157 Sequence pairs did not map uniquely: 5564 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: 4532 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4747 ((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: 273135 Total methylated C's in CpG context: 10316 Total methylated C's in CHG context: 1813 Total methylated C's in CHH context: 67941 Total methylated C's in Unknown context: 825 Total unmethylated C's in CpG context: 21844 Total unmethylated C's in CHG context: 42822 Total unmethylated C's in CHH context: 128399 Total unmethylated C's in Unknown context: 1183 C methylated in CpG context: 32.1% C methylated in CHG context: 4.1% C methylated in CHH context: 34.6% C methylated in unknown context (CN or CHN): 41.1% Bismark completed in 0d 0h 1m 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/dumoar/scaff-genome/ (absolute path is '/gscratch/srlab/sr320/data/dumoar/scaff-genome/)' FastQ format assumed (by default) Processing sequences up to read no. 40000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 40 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/031223-sc-17'): /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R1_001_val_1.fq.gz /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_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 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/031223-sc-17 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/dumoar/scaff-genome/ chr PGA_scaffold0__40_contigs__length_4818635 (4818635 bp) chr PGA_scaffold1__111_contigs__length_23635802 (23635802 bp) chr PGA_scaffold2__216_contigs__length_42616187 (42616187 bp) chr PGA_scaffold3__77_contigs__length_22140449 (22140449 bp) chr PGA_scaffold4__118_contigs__length_24133938 (24133938 bp) chr PGA_scaffold5__54_contigs__length_17529967 (17529967 bp) chr PGA_scaffold6__2_contigs__length_4500 (4500 bp) chr PGA_scaffold7__77_contigs__length_16129408 (16129408 bp) chr PGA_scaffold8__70_contigs__length_6254265 (6254265 bp) chr PGA_scaffold9__2_contigs__length_6774 (6774 bp) chr PGA_scaffold10__58_contigs__length_8083807 (8083807 bp) chr PGA_scaffold11__78_contigs__length_11409253 (11409253 bp) chr PGA_scaffold12__214_contigs__length_38711105 (38711105 bp) chr PGA_scaffold13__56_contigs__length_10281103 (10281103 bp) chr PGA_scaffold14__49_contigs__length_6382615 (6382615 bp) chr PGA_scaffold15__74_contigs__length_14466968 (14466968 bp) chr PGA_scaffold16__99_contigs__length_13714835 (13714835 bp) chr PGA_scaffold17__171_contigs__length_27881435 (27881435 bp) chr PGA_scaffold18__98_contigs__length_15388888 (15388888 bp) chr PGA_scaffold19__65_contigs__length_13296201 (13296201 bp) chr PGA_scaffold20__42_contigs__length_7444180 (7444180 bp) chr PGA_scaffold21__67_contigs__length_16858916 (16858916 bp) chr PGA_scaffold22__59_contigs__length_10008237 (10008237 bp) chr PGA_scaffold23__65_contigs__length_9586800 (9586800 bp) chr PGA_scaffold24__25_contigs__length_9615596 (9615596 bp) chr PGA_scaffold25__121_contigs__length_9021638 (9021638 bp) chr PGA_scaffold26__34_contigs__length_3174094 (3174094 bp) chr PGA_scaffold27__24_contigs__length_4511419 (4511419 bp) chr PGA_scaffold28__73_contigs__length_10794191 (10794191 bp) chr PGA_scaffold29__63_contigs__length_7458616 (7458616 bp) chr PGA_scaffold30__53_contigs__length_3533588 (3533588 bp) chr PGA_scaffold31__35_contigs__length_1951197 (1951197 bp) chr PGA_scaffold32__48_contigs__length_8091588 (8091588 bp) chr PGA_scaffold33__68_contigs__length_5591008 (5591008 bp) chr PGA_scaffold34__18_contigs__length_2048619 (2048619 bp) chr PGA_scaffold35__36_contigs__length_7416912 (7416912 bp) chr PGA_scaffold36__50_contigs__length_8312113 (8312113 bp) chr PGA_scaffold37__114_contigs__length_22981779 (22981779 bp) chr PGA_scaffold38__30_contigs__length_10707134 (10707134 bp) chr PGA_scaffold39__82_contigs__length_19157343 (19157343 bp) chr PGA_scaffold40__81_contigs__length_9975379 (9975379 bp) chr PGA_scaffold41__67_contigs__length_15779270 (15779270 bp) chr PGA_scaffold42__119_contigs__length_25812110 (25812110 bp) chr PGA_scaffold43__161_contigs__length_26349757 (26349757 bp) chr PGA_scaffold44__101_contigs__length_25971783 (25971783 bp) chr PGA_scaffold45__51_contigs__length_13476971 (13476971 bp) chr PGA_scaffold46__73_contigs__length_12693875 (12693875 bp) chr PGA_scaffold47__164_contigs__length_21858264 (21858264 bp) chr PGA_scaffold48__117_contigs__length_14149252 (14149252 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file CH10_11_S20_L001_R1_001_val_1.fq.gz to CH10_11_S20_L001_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file CH10_11_S20_L001_R1_001_val_1.fq.gz (40001 sequences in total) Processing reads up to sequence no. 40000 from /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file CH10_11_S20_L001_R2_001_val_2.fq.gz to CH10_11_S20_L001_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file CH10_11_S20_L001_R2_001_val_2.fq.gz (40001 sequences in total) Input files are CH10_11_S20_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH10_11_S20_L001_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/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CH10_11_S20_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH10_11_S20_L001_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: K00337:412:HKTCJBBXY:1:1101:3579:1367_1:N:0:NAGTGG/1 77 * 0 0 * * 0 0 AATTTAAATAGTATTTGGATTTGTTTATGGTGGATTGGGTTGAGTGT JJFJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFF YT:Z:UP K00337:412:HKTCJBBXY:1:1101:3579:1367_2:N:0:NAGTGG/2 141 * 0 0 * * 0 0 ACACTCAACCCAATCCACCATAAACAAATCCAAATACTATTTAAATT JJJJFJJJJJJAJ7JJJJJJ-FAJAJJFFJJJJ7-F-->> Writing bisulfite mapping results to CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R2_001_val_2.fq.gz 40000 reads; of these: 40000 (100.00%) were paired; of these: 28292 (70.73%) aligned concordantly 0 times 4674 (11.69%) aligned concordantly exactly 1 time 7034 (17.59%) aligned concordantly >1 times 29.27% overall alignment rate 40000 reads; of these: 40000 (100.00%) were paired; of these: 28265 (70.66%) aligned concordantly 0 times 4659 (11.65%) aligned concordantly exactly 1 time 7076 (17.69%) aligned concordantly >1 times 29.34% overall alignment rate Processed 40000 sequences in total Successfully deleted the temporary files CH10_11_S20_L001_R1_001_val_1.fq.gz_C_to_T.fastq and CH10_11_S20_L001_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40000 Number of paired-end alignments with a unique best hit: 11301 Mapping efficiency: 28.3% Sequence pairs with no alignments under any condition: 23747 Sequence pairs did not map uniquely: 4952 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: 5587 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5714 ((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: 341524 Total methylated C's in CpG context: 32276 Total methylated C's in CHG context: 1958 Total methylated C's in CHH context: 37873 Total methylated C's in Unknown context: 589 Total unmethylated C's in CpG context: 15937 Total unmethylated C's in CHG context: 63203 Total unmethylated C's in CHH context: 190277 Total unmethylated C's in Unknown context: 1399 C methylated in CpG context: 66.9% C methylated in CHG context: 3.0% C methylated in CHH context: 16.6% C methylated in unknown context (CN or CHN): 29.6% Bismark completed in 0d 0h 1m 1s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): CH01_06_S1_L001_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 >>CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.bam: 10749 Total number duplicated alignments removed: 1840 (17.12%) Duplicated alignments were found at: 1388 different position(s) Total count of deduplicated leftover sequences: 8909 (82.88% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH01_14_S2_L001_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 >>CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.bam: 10453 Total number duplicated alignments removed: 1973 (18.87%) Duplicated alignments were found at: 1499 different position(s) Total count of deduplicated leftover sequences: 8480 (81.13% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH01_22_S3_L001_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 >>CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.bam: 11096 Total number duplicated alignments removed: 1884 (16.98%) Duplicated alignments were found at: 1474 different position(s) Total count of deduplicated leftover sequences: 9212 (83.02% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH01_38_S4_L001_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 >>CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.bam: 10756 Total number duplicated alignments removed: 1860 (17.29%) Duplicated alignments were found at: 1460 different position(s) Total count of deduplicated leftover sequences: 8896 (82.71% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH03_04_S5_L001_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 >>CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.bam: 8170 Total number duplicated alignments removed: 1092 (13.37%) Duplicated alignments were found at: 866 different position(s) Total count of deduplicated leftover sequences: 7078 (86.63% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH03_15_S6_L001_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 >>CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.bam: 7805 Total number duplicated alignments removed: 1420 (18.19%) Duplicated alignments were found at: 1101 different position(s) Total count of deduplicated leftover sequences: 6385 (81.81% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH03_33_S7_L001_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 >>CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.bam: 10579 Total number duplicated alignments removed: 1929 (18.23%) Duplicated alignments were found at: 1479 different position(s) Total count of deduplicated leftover sequences: 8650 (81.77% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH05_01_S8_L001_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 >>CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.bam: 9690 Total number duplicated alignments removed: 1463 (15.10%) Duplicated alignments were found at: 1159 different position(s) Total count of deduplicated leftover sequences: 8227 (84.90% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH05_06_S9_L001_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 >>CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.bam: 7446 Total number duplicated alignments removed: 1315 (17.66%) Duplicated alignments were found at: 965 different position(s) Total count of deduplicated leftover sequences: 6131 (82.34% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH05_21_S10_L001_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 >>CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.bam: 11042 Total number duplicated alignments removed: 2204 (19.96%) Duplicated alignments were found at: 1655 different position(s) Total count of deduplicated leftover sequences: 8838 (80.04% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH05_24_S11_L001_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 >>CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.bam: 11605 Total number duplicated alignments removed: 2059 (17.74%) Duplicated alignments were found at: 1568 different position(s) Total count of deduplicated leftover sequences: 9546 (82.26% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH07_06_S12_L001_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 >>CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.bam: 10586 Total number duplicated alignments removed: 1900 (17.95%) Duplicated alignments were found at: 1447 different position(s) Total count of deduplicated leftover sequences: 8686 (82.05% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH07_11_S13_L001_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 >>CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.bam: 7454 Total number duplicated alignments removed: 1360 (18.25%) Duplicated alignments were found at: 994 different position(s) Total count of deduplicated leftover sequences: 6094 (81.75% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH07_24_S14_L001_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 >>CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.bam: 8520 Total number duplicated alignments removed: 1348 (15.82%) Duplicated alignments were found at: 1059 different position(s) Total count of deduplicated leftover sequences: 7172 (84.18% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH09_02_S15_L001_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 >>CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.bam: 11144 Total number duplicated alignments removed: 1839 (16.50%) Duplicated alignments were found at: 1453 different position(s) Total count of deduplicated leftover sequences: 9305 (83.50% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH09_13_S16_L001_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 >>CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.bam: 11691 Total number duplicated alignments removed: 2053 (17.56%) Duplicated alignments were found at: 1537 different position(s) Total count of deduplicated leftover sequences: 9638 (82.44% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH09_28_S17_L001_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 >>CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.bam: 10849 Total number duplicated alignments removed: 2021 (18.63%) Duplicated alignments were found at: 1575 different position(s) Total count of deduplicated leftover sequences: 8828 (81.37% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH10_01_S18_L001_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 >>CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.bam: 11202 Total number duplicated alignments removed: 1776 (15.85%) Duplicated alignments were found at: 1428 different position(s) Total count of deduplicated leftover sequences: 9426 (84.15% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH10_08_S19_L001_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 >>CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.bam: 9279 Total number duplicated alignments removed: 1323 (14.26%) Duplicated alignments were found at: 1019 different position(s) Total count of deduplicated leftover sequences: 7956 (85.74% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): CH10_11_S20_L001_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 >>CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.bam: 11301 Total number duplicated alignments removed: 1983 (17.55%) Duplicated alignments were found at: 1543 different position(s) Total count of deduplicated leftover sequences: 9318 (82.45% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R2_001_val_2.fq.gz" *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file CH01_06_S1_L001_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 Core usage currently set to more than 20 threads. Let's see how this goes... (set value: 28) Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 28 Strand-specific outputs will be skipped. Separate output files for cytosines in CpG, CHG and CHH context will be generated Merge CHG and CHH context to non-CpG context specified Output will be written to the current directory ('/gscratch/scrubbed/sr320/031223-sc-17') 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 >>CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH01_06_S1_L001_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 to CpG_context_CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_06_S1_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 8909 lines in total Total number of methylation call strings processed: 17818 Final Cytosine Methylation Report ================================= Total number of C's analysed: 168782 Total methylated C's in CpG context: 21081 Total methylated C's in CHG context: 854 Total methylated C's in CHH context: 14267 Total C to T conversions in CpG context: 7485 Total C to T conversions in CHG context: 33316 Total C to T conversions in CHH context: 91779 C methylated in CpG context: 73.8% C methylated in non-CpG context: 10.8% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH01_06_S1_L001_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/sr320/031223-sc-17/CpG_context_CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH01_14_S2_L001_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 to CpG_context_CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_14_S2_L001_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 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_14_S2_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 8480 lines in total Total number of methylation call strings processed: 16960 Final Cytosine Methylation Report ================================= Total number of C's analysed: 135244 Total methylated C's in CpG context: 13149 Total methylated C's in CHG context: 713 Total methylated C's in CHH context: 15510 Total C to T conversions in CpG context: 6324 Total C to T conversions in CHG context: 23621 Total C to T conversions in CHH context: 75927 C methylated in CpG context: 67.5% C methylated in non-CpG context: 14.0% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH01_14_S2_L001_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/sr320/031223-sc-17/CpG_context_CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH01_22_S3_L001_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 to CpG_context_CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_22_S3_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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.. Merging individual splitting reports into overall report: 'CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 9212 lines in total Total number of methylation call strings processed: 18424 Final Cytosine Methylation Report ================================= Total number of C's analysed: 172593 Total methylated C's in CpG context: 17142 Total methylated C's in CHG context: 828 Total methylated C's in CHH context: 15071 Total C to T conversions in CpG context: 8815 Total C to T conversions in CHG context: 32711 Total C to T conversions in CHH context: 98026 C methylated in CpG context: 66.0% C methylated in non-CpG context: 10.8% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH01_22_S3_L001_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/sr320/031223-sc-17/CpG_context_CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH01_38_S4_L001_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 to CpG_context_CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_38_S4_L001_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 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_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 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH01_38_S4_L001_R2_001_val_2.fq.gz" Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 8896 lines in total Total number of methylation call strings processed: 17792 Final Cytosine Methylation Report ================================= Total number of C's analysed: 144407 Total methylated C's in CpG context: 13962 Total methylated C's in CHG context: 874 Total methylated C's in CHH context: 17873 Total C to T conversions in CpG context: 6787 Total C to T conversions in CHG context: 26656 Total C to T conversions in CHH context: 78255 C methylated in CpG context: 67.3% C methylated in non-CpG context: 15.2% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH01_38_S4_L001_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/sr320/031223-sc-17/CpG_context_CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH03_04_S5_L001_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 to CpG_context_CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH03_04_S5_L001_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 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_04_S5_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 7078 lines in total Total number of methylation call strings processed: 14156 Final Cytosine Methylation Report ================================= Total number of C's analysed: 109311 Total methylated C's in CpG context: 1448 Total methylated C's in CHG context: 668 Total methylated C's in CHH context: 36515 Total C to T conversions in CpG context: 10823 Total C to T conversions in CHG context: 13419 Total C to T conversions in CHH context: 46438 C methylated in CpG context: 11.8% C methylated in non-CpG context: 38.3% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH03_04_S5_L001_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/sr320/031223-sc-17/CpG_context_CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH03_15_S6_L001_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 to CpG_context_CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH03_15_S6_L001_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 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_15_S6_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 6385 lines in total Total number of methylation call strings processed: 12770 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114318 Total methylated C's in CpG context: 2977 Total methylated C's in CHG context: 559 Total methylated C's in CHH context: 20227 Total C to T conversions in CpG context: 12097 Total C to T conversions in CHG context: 17712 Total C to T conversions in CHH context: 60746 C methylated in CpG context: 19.7% C methylated in non-CpG context: 20.9% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH03_15_S6_L001_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/sr320/031223-sc-17/CpG_context_CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH03_33_S7_L001_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 to CpG_context_CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH03_33_S7_L001_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 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH03_33_S7_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 8650 lines in total Total number of methylation call strings processed: 17300 Final Cytosine Methylation Report ================================= Total number of C's analysed: 178767 Total methylated C's in CpG context: 21761 Total methylated C's in CHG context: 921 Total methylated C's in CHH context: 13420 Total C to T conversions in CpG context: 7995 Total C to T conversions in CHG context: 35844 Total C to T conversions in CHH context: 98826 C methylated in CpG context: 73.1% C methylated in non-CpG context: 9.6% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH03_33_S7_L001_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/sr320/031223-sc-17/CpG_context_CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH05_01_S8_L001_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 to CpG_context_CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_01_S8_L001_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 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_01_S8_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 8227 lines in total Total number of methylation call strings processed: 16454 Final Cytosine Methylation Report ================================= Total number of C's analysed: 126279 Total methylated C's in CpG context: 7610 Total methylated C's in CHG context: 799 Total methylated C's in CHH context: 31099 Total C to T conversions in CpG context: 7672 Total C to T conversions in CHG context: 19815 Total C to T conversions in CHH context: 59284 C methylated in CpG context: 49.8% C methylated in non-CpG context: 28.7% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH05_01_S8_L001_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/sr320/031223-sc-17/CpG_context_CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH05_06_S9_L001_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 to CpG_context_CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_06_S9_L001_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 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_06_S9_L001_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 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_06_S9_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 6131 lines in total Total number of methylation call strings processed: 12262 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128426 Total methylated C's in CpG context: 1195 Total methylated C's in CHG context: 467 Total methylated C's in CHH context: 17120 Total C to T conversions in CpG context: 14635 Total C to T conversions in CHG context: 19842 Total C to T conversions in CHH context: 75167 C methylated in CpG context: 7.5% C methylated in non-CpG context: 15.6% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH05_06_S9_L001_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/sr320/031223-sc-17/CpG_context_CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH05_21_S10_L001_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 to CpG_context_CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_21_S10_L001_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 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_21_S10_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 8838 lines in total Total number of methylation call strings processed: 17676 Final Cytosine Methylation Report ================================= Total number of C's analysed: 164008 Total methylated C's in CpG context: 14032 Total methylated C's in CHG context: 923 Total methylated C's in CHH context: 24588 Total C to T conversions in CpG context: 8179 Total C to T conversions in CHG context: 29710 Total C to T conversions in CHH context: 86576 C methylated in CpG context: 63.2% C methylated in non-CpG context: 18.0% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH05_21_S10_L001_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/sr320/031223-sc-17/CpG_context_CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH05_24_S11_L001_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 to CpG_context_CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_24_S11_L001_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 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH05_24_S11_L001_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 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH05_24_S11_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 9546 lines in total Total number of methylation call strings processed: 19092 Final Cytosine Methylation Report ================================= Total number of C's analysed: 155000 Total methylated C's in CpG context: 17515 Total methylated C's in CHG context: 1083 Total methylated C's in CHH context: 22808 Total C to T conversions in CpG context: 6968 Total C to T conversions in CHG context: 29638 Total C to T conversions in CHH context: 76988 C methylated in CpG context: 71.5% C methylated in non-CpG context: 18.3% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH05_24_S11_L001_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/sr320/031223-sc-17/CpG_context_CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH07_06_S12_L001_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 to CpG_context_CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH07_06_S12_L001_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 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH07_06_S12_L001_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 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_06_S12_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 8686 lines in total Total number of methylation call strings processed: 17372 Final Cytosine Methylation Report ================================= Total number of C's analysed: 164386 Total methylated C's in CpG context: 16239 Total methylated C's in CHG context: 942 Total methylated C's in CHH context: 18539 Total C to T conversions in CpG context: 9022 Total C to T conversions in CHG context: 30255 Total C to T conversions in CHH context: 89389 C methylated in CpG context: 64.3% C methylated in non-CpG context: 14.0% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH07_06_S12_L001_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/sr320/031223-sc-17/CpG_context_CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH07_11_S13_L001_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 to CpG_context_CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_11_S13_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 6094 lines in total Total number of methylation call strings processed: 12188 Final Cytosine Methylation Report ================================= Total number of C's analysed: 120655 Total methylated C's in CpG context: 1238 Total methylated C's in CHG context: 645 Total methylated C's in CHH context: 15719 Total C to T conversions in CpG context: 13303 Total C to T conversions in CHG context: 18904 Total C to T conversions in CHH context: 70846 C methylated in CpG context: 8.5% C methylated in non-CpG context: 15.4% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH07_11_S13_L001_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/sr320/031223-sc-17/CpG_context_CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH07_24_S14_L001_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 to CpG_context_CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH07_24_S14_L001_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 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH07_24_S14_L001_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 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 7172 lines in total Total number of methylation call strings processed: 14344 Final Cytosine Methylation Report ================================= Total number of C's analysed: 138533 Total methylated C's in CpG context: 1088 Total methylated C's in CHG context: 513 Total methylated C's in CHH context: 17978 Total C to T conversions in CpG context: 13819 Total C to T conversions in CHG context: 18500 Total C to T conversions in CHH context: 86635 C methylated in CpG context: 7.3% C methylated in non-CpG context: 15.0% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH07_24_S14_L001_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/sr320/031223-sc-17/CpG_context_CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH09_02_S15_L001_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 to CpG_context_CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH09_02_S15_L001_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 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_02_S15_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 9305 lines in total Total number of methylation call strings processed: 18610 Final Cytosine Methylation Report ================================= Total number of C's analysed: 146989 Total methylated C's in CpG context: 13923 Total methylated C's in CHG context: 967 Total methylated C's in CHH context: 23372 Total C to T conversions in CpG context: 6566 Total C to T conversions in CHG context: 24613 Total C to T conversions in CHH context: 77548 C methylated in CpG context: 68.0% C methylated in non-CpG context: 19.2% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH09_02_S15_L001_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/sr320/031223-sc-17/CpG_context_CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH09_13_S16_L001_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 to CpG_context_CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH09_13_S16_L001_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 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_13_S16_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 9638 lines in total Total number of methylation call strings processed: 19276 Final Cytosine Methylation Report ================================= Total number of C's analysed: 195511 Total methylated C's in CpG context: 10484 Total methylated C's in CHG context: 913 Total methylated C's in CHH context: 24109 Total C to T conversions in CpG context: 11037 Total C to T conversions in CHG context: 31121 Total C to T conversions in CHH context: 117847 C methylated in CpG context: 48.7% C methylated in non-CpG context: 14.4% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH09_13_S16_L001_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/sr320/031223-sc-17/CpG_context_CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH09_28_S17_L001_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 to CpG_context_CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH09_28_S17_L001_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 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH09_28_S17_L001_R2_001_val_2.fq.gz" Now reading in Bismark result file CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 8828 lines in total Total number of methylation call strings processed: 17656 Final Cytosine Methylation Report ================================= Total number of C's analysed: 162498 Total methylated C's in CpG context: 16200 Total methylated C's in CHG context: 1230 Total methylated C's in CHH context: 18066 Total C to T conversions in CpG context: 7845 Total C to T conversions in CHG context: 30912 Total C to T conversions in CHH context: 88245 C methylated in CpG context: 67.4% C methylated in non-CpG context: 13.9% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH09_28_S17_L001_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/sr320/031223-sc-17/CpG_context_CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH10_01_S18_L001_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 to CpG_context_CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_01_S18_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 9426 lines in total Total number of methylation call strings processed: 18852 Final Cytosine Methylation Report ================================= Total number of C's analysed: 164305 Total methylated C's in CpG context: 17292 Total methylated C's in CHG context: 1073 Total methylated C's in CHH context: 17231 Total C to T conversions in CpG context: 7026 Total C to T conversions in CHG context: 30934 Total C to T conversions in CHH context: 90749 C methylated in CpG context: 71.1% C methylated in non-CpG context: 13.1% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH10_01_S18_L001_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/sr320/031223-sc-17/CpG_context_CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH10_08_S19_L001_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 to CpG_context_CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_08_S19_L001_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 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_08_S19_L001_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 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_08_S19_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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: 'CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 7956 lines in total Total number of methylation call strings processed: 15912 Final Cytosine Methylation Report ================================= Total number of C's analysed: 128614 Total methylated C's in CpG context: 4466 Total methylated C's in CHG context: 853 Total methylated C's in CHH context: 36046 Total C to T conversions in CpG context: 9817 Total C to T conversions in CHG context: 18524 Total C to T conversions in CHH context: 58908 C methylated in CpG context: 31.3% C methylated in non-CpG context: 32.3% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH10_08_S19_L001_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/sr320/031223-sc-17/CpG_context_CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Checking file >>CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >CH10_11_S20_L001_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 to CpG_context_CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_11_S20_L001_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 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_11_S20_L001_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 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file CH10_11_S20_L001_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 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file CH10_11_S20_L001_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:PGA_scaffold0__40_contigs__length_4818635 LN:4818635 skipping SAM header line: @SQ SN:PGA_scaffold1__111_contigs__length_23635802 LN:23635802 skipping SAM header line: @SQ SN:PGA_scaffold2__216_contigs__length_42616187 LN:42616187 skipping SAM header line: @SQ SN:PGA_scaffold3__77_contigs__length_22140449 LN:22140449 skipping SAM header line: @SQ SN:PGA_scaffold4__118_contigs__length_24133938 LN:24133938 skipping SAM header line: @SQ SN:PGA_scaffold5__54_contigs__length_17529967 LN:17529967 skipping SAM header line: @SQ SN:PGA_scaffold6__2_contigs__length_4500 LN:4500 skipping SAM header line: @SQ SN:PGA_scaffold7__77_contigs__length_16129408 LN:16129408 skipping SAM header line: @SQ SN:PGA_scaffold8__70_contigs__length_6254265 LN:6254265 skipping SAM header line: @SQ SN:PGA_scaffold9__2_contigs__length_6774 LN:6774 skipping SAM header line: @SQ SN:PGA_scaffold10__58_contigs__length_8083807 LN:8083807 skipping SAM header line: @SQ SN:PGA_scaffold11__78_contigs__length_11409253 LN:11409253 skipping SAM header line: @SQ SN:PGA_scaffold12__214_contigs__length_38711105 LN:38711105 skipping SAM header line: @SQ SN:PGA_scaffold13__56_contigs__length_10281103 LN:10281103 skipping SAM header line: @SQ SN:PGA_scaffold14__49_contigs__length_6382615 LN:6382615 skipping SAM header line: @SQ SN:PGA_scaffold15__74_contigs__length_14466968 LN:14466968 skipping SAM header line: @SQ SN:PGA_scaffold16__99_contigs__length_13714835 LN:13714835 skipping SAM header line: @SQ SN:PGA_scaffold17__171_contigs__length_27881435 LN:27881435 skipping SAM header line: @SQ SN:PGA_scaffold18__98_contigs__length_15388888 LN:15388888 skipping SAM header line: @SQ SN:PGA_scaffold19__65_contigs__length_13296201 LN:13296201 skipping SAM header line: @SQ SN:PGA_scaffold20__42_contigs__length_7444180 LN:7444180 skipping SAM header line: @SQ SN:PGA_scaffold21__67_contigs__length_16858916 LN:16858916 skipping SAM header line: @SQ SN:PGA_scaffold22__59_contigs__length_10008237 LN:10008237 skipping SAM header line: @SQ SN:PGA_scaffold23__65_contigs__length_9586800 LN:9586800 skipping SAM header line: @SQ SN:PGA_scaffold24__25_contigs__length_9615596 LN:9615596 skipping SAM header line: @SQ SN:PGA_scaffold25__121_contigs__length_9021638 LN:9021638 skipping SAM header line: @SQ SN:PGA_scaffold26__34_contigs__length_3174094 LN:3174094 skipping SAM header line: @SQ SN:PGA_scaffold27__24_contigs__length_4511419 LN:4511419 skipping SAM header line: @SQ SN:PGA_scaffold28__73_contigs__length_10794191 LN:10794191 skipping SAM header line: @SQ SN:PGA_scaffold29__63_contigs__length_7458616 LN:7458616 skipping SAM header line: @SQ SN:PGA_scaffold30__53_contigs__length_3533588 LN:3533588 skipping SAM header line: @SQ SN:PGA_scaffold31__35_contigs__length_1951197 LN:1951197 skipping SAM header line: @SQ SN:PGA_scaffold32__48_contigs__length_8091588 LN:8091588 skipping SAM header line: @SQ SN:PGA_scaffold33__68_contigs__length_5591008 LN:5591008 skipping SAM header line: @SQ SN:PGA_scaffold34__18_contigs__length_2048619 LN:2048619 skipping SAM header line: @SQ SN:PGA_scaffold35__36_contigs__length_7416912 LN:7416912 skipping SAM header line: @SQ SN:PGA_scaffold36__50_contigs__length_8312113 LN:8312113 skipping SAM header line: @SQ SN:PGA_scaffold37__114_contigs__length_22981779 LN:22981779 skipping SAM header line: @SQ SN:PGA_scaffold38__30_contigs__length_10707134 LN:10707134 skipping SAM header line: @SQ SN:PGA_scaffold39__82_contigs__length_19157343 LN:19157343 skipping SAM header line: @SQ SN:PGA_scaffold40__81_contigs__length_9975379 LN:9975379 skipping SAM header line: @SQ SN:PGA_scaffold41__67_contigs__length_15779270 LN:15779270 skipping SAM header line: @SQ SN:PGA_scaffold42__119_contigs__length_25812110 LN:25812110 skipping SAM header line: @SQ SN:PGA_scaffold43__161_contigs__length_26349757 LN:26349757 skipping SAM header line: @SQ SN:PGA_scaffold44__101_contigs__length_25971783 LN:25971783 skipping SAM header line: @SQ SN:PGA_scaffold45__51_contigs__length_13476971 LN:13476971 skipping SAM header line: @SQ SN:PGA_scaffold46__73_contigs__length_12693875 LN:12693875 skipping SAM header line: @SQ SN:PGA_scaffold47__164_contigs__length_21858264 LN:21858264 skipping SAM header line: @SQ SN:PGA_scaffold48__117_contigs__length_14149252 LN:14149252 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/dumoar/scaff-genome/ -u 40000 -p 40 -score_min L,0,-0.6 -1 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R1_001_val_1.fq.gz -2 /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH10_11_S20_L001_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished 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: 'CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 9318 lines in total Total number of methylation call strings processed: 18636 Final Cytosine Methylation Report ================================= Total number of C's analysed: 149633 Total methylated C's in CpG context: 13408 Total methylated C's in CHG context: 910 Total methylated C's in CHH context: 18632 Total C to T conversions in CpG context: 6916 Total C to T conversions in CHG context: 26372 Total C to T conversions in CHH context: 83395 C methylated in CpG context: 66.0% C methylated in non-CpG context: 15.1% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 131 Maximum read length of Read 2: 131 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: 131 Maximum read length of Read 2: 131 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_context_CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Non_CpG_context_CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_context_CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: CH10_11_S20_L001_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/sr320/031223-sc-17/CpG_context_CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Sorting everything in memory instead of writing out individual chromosome files ... Sorting input file CpG_context_CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.txt by positions (using -S of 75%) Finished BedGraph conversion ... Found 20 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> CH01_06_S1_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH01_06_S1_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH01_06_S1_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH01_06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH01_14_S2_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH01_14_S2_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH01_14_S2_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH01_14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH01_22_S3_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH01_22_S3_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH01_22_S3_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH01_22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH01_38_S4_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH01_38_S4_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH01_38_S4_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH01_38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH03_04_S5_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH03_04_S5_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH03_04_S5_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH03_04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH03_15_S6_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH03_15_S6_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH03_15_S6_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH03_15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH03_33_S7_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH03_33_S7_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH03_33_S7_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH03_33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH05_01_S8_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH05_01_S8_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH05_01_S8_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH05_01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH05_06_S9_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH05_06_S9_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH05_06_S9_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH05_06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH05_21_S10_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH05_21_S10_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH05_21_S10_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH05_21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH05_24_S11_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH05_24_S11_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH05_24_S11_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH05_24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH07_06_S12_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH07_06_S12_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH07_06_S12_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH07_06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH07_11_S13_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH07_11_S13_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH07_11_S13_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH07_11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH07_24_S14_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH07_24_S14_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH07_24_S14_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH07_24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH09_02_S15_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH09_02_S15_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH09_02_S15_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH09_02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH09_13_S16_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH09_13_S16_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH09_13_S16_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH09_13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH09_28_S17_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH09_28_S17_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH09_28_S17_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH09_28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH10_01_S18_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH10_01_S18_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH10_01_S18_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH10_01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH10_08_S19_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH10_08_S19_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH10_08_S19_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH10_08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> CH10_11_S20_L001_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > CH10_11_S20_L001_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report CH10_11_S20_L001_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report CH10_11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 20 Bismark BAM file(s)... >> Reading from Bismark report: CH01_06_S1_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH01_14_S2_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH01_22_S3_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH01_38_S4_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH03_04_S5_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH03_15_S6_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH03_33_S7_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH05_01_S8_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH05_06_S9_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH05_21_S10_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH05_24_S11_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH07_06_S12_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH07_11_S13_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH07_24_S14_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH09_02_S15_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH09_13_S16_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH09_28_S17_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH10_01_S18_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH10_08_S19_L001_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: CH10_11_S20_L001_R1_001_val_1_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html <<