Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' FastQ format assumed (by default) 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1024'): /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R1_val_1.fq.gz /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R2_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) Current working directory is: /gscratch/srlab/sr320/analyses/1024 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_10_s1_R1_val_1.fq.gz to zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file zr2096_10_s1_R1_val_1.fq.gz (17448883 sequences in total) Writing a G -> A converted version of the input file zr2096_10_s1_R2_val_2.fq.gz to zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file zr2096_10_s1_R2_val_2.fq.gz (17448883 sequences in total) Input files are zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_10_s1_R2_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:2:1101:1232:2155_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 ATTGTATTAATTATAAAAAATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTTATTATTAAAAATATTAAATA FFFFFFFFFBFFFFFFFFFFFFF#################################<>> Writing bisulfite mapping results to zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far 17448883 reads; of these: 17448883 (100.00%) were paired; of these: 11356756 (65.09%) aligned concordantly 0 times 2277521 (13.05%) aligned concordantly exactly 1 time 3814606 (21.86%) aligned concordantly >1 times 34.91% overall alignment rate 17448883 reads; of these: 17448883 (100.00%) were paired; of these: 11364097 (65.13%) aligned concordantly 0 times 2265117 (12.98%) aligned concordantly exactly 1 time 3819669 (21.89%) aligned concordantly >1 times 34.87% overall alignment rate Processed 17448883 sequences in total Successfully deleted the temporary files zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 17448883 Number of paired-end alignments with a unique best hit: 6101640 Mapping efficiency: 35.0% Sequence pairs with no alignments under any condition: 9119335 Sequence pairs did not map uniquely: 2227908 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: 3051408 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3050232 ((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: 155361061 Total methylated C's in CpG context: 14429916 Total methylated C's in CHG context: 2478416 Total methylated C's in CHH context: 18074812 Total methylated C's in Unknown context: 901290 Total unmethylated C's in CpG context: 5602290 Total unmethylated C's in CHG context: 28295170 Total unmethylated C's in CHH context: 86480457 Total unmethylated C's in Unknown context: 2099324 C methylated in CpG context: 72.0% C methylated in CHG context: 8.1% C methylated in CHH context: 17.3% C methylated in unknown context (CN or CHN): 30.0% Bismark completed in 0d 2h 27m 59s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' FastQ format assumed (by default) 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1024'): /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R1_val_1.fq.gz /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R2_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) Current working directory is: /gscratch/srlab/sr320/analyses/1024 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_1_s1_R1_val_1.fq.gz to zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file zr2096_1_s1_R1_val_1.fq.gz (28603346 sequences in total) Writing a G -> A converted version of the input file zr2096_1_s1_R2_val_2.fq.gz to zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file zr2096_1_s1_R2_val_2.fq.gz (28603346 sequences in total) Input files are zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_1_s1_R2_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1249:2156_1:N:0:CGATGT/1 99 NC_035783.1_CT_converted 37030813 1 79M = 37030917 184 GATTATTTGTTGTTTGTTGTTTGTTTGNNNNTNNNTNNGTTTGTTTGTTTGTTTGTTTGTTTGTAAATTTTTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<##<<>> Writing bisulfite mapping results to zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R2_val_2.fq.gz Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1104:3705:43673_1:N:0:CGATGT NC_035780.1 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far 28603346 reads; of these: 28603346 (100.00%) were paired; of these: 23409579 (81.84%) aligned concordantly 0 times 1855802 (6.49%) aligned concordantly exactly 1 time 3337965 (11.67%) aligned concordantly >1 times 18.16% overall alignment rate 28603346 reads; of these: 28603346 (100.00%) were paired; of these: 23380286 (81.74%) aligned concordantly 0 times 1861809 (6.51%) aligned concordantly exactly 1 time 3361251 (11.75%) aligned concordantly >1 times 18.26% overall alignment rate Processed 28603346 sequences in total Successfully deleted the temporary files zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28603346 Number of paired-end alignments with a unique best hit: 5210642 Mapping efficiency: 18.2% Sequence pairs with no alignments under any condition: 21591441 Sequence pairs did not map uniquely: 1801263 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2629242 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2581399 ((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: 120268705 Total methylated C's in CpG context: 9580406 Total methylated C's in CHG context: 1920364 Total methylated C's in CHH context: 17770842 Total methylated C's in Unknown context: 1187244 Total unmethylated C's in CpG context: 3836175 Total unmethylated C's in CHG context: 19131376 Total unmethylated C's in CHH context: 68029542 Total unmethylated C's in Unknown context: 2236683 C methylated in CpG context: 71.4% C methylated in CHG context: 9.1% C methylated in CHH context: 20.7% C methylated in unknown context (CN or CHN): 34.7% Bismark completed in 0d 2h 27m 15s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' FastQ format assumed (by default) 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1024'): /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R1_val_1.fq.gz /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R2_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) Current working directory is: /gscratch/srlab/sr320/analyses/1024 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_2_s1_R1_val_1.fq.gz to zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file zr2096_2_s1_R1_val_1.fq.gz (30325606 sequences in total) Writing a G -> A converted version of the input file zr2096_2_s1_R2_val_2.fq.gz to zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file zr2096_2_s1_R2_val_2.fq.gz (30325606 sequences in total) Input files are zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_2_s1_R2_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1148:2157_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 AAATTTATTATTTTAAAAATAAAAATTNNNNTNNNTTTTATTATTTTTTTTAATATTTTTTAATATAATTAAATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<<>> Writing bisulfite mapping results to zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1316:4047:74652_1:N:0:TGACCA NC_007175.2 17170 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far 30325606 reads; of these: 30325606 (100.00%) were paired; of these: 19324232 (63.72%) aligned concordantly 0 times 3832152 (12.64%) aligned concordantly exactly 1 time 7169222 (23.64%) aligned concordantly >1 times 36.28% overall alignment rate 30325606 reads; of these: 30325606 (100.00%) were paired; of these: 19331894 (63.75%) aligned concordantly 0 times 3841082 (12.67%) aligned concordantly exactly 1 time 7152630 (23.59%) aligned concordantly >1 times 36.25% overall alignment rate Processed 30325606 sequences in total Successfully deleted the temporary files zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 30325606 Number of paired-end alignments with a unique best hit: 10644443 Mapping efficiency: 35.1% Sequence pairs with no alignments under any condition: 15589998 Sequence pairs did not map uniquely: 4091165 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5330944 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5313498 ((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: 240863373 Total methylated C's in CpG context: 20849160 Total methylated C's in CHG context: 3871921 Total methylated C's in CHH context: 34921070 Total methylated C's in Unknown context: 2003079 Total unmethylated C's in CpG context: 7639660 Total unmethylated C's in CHG context: 41649721 Total unmethylated C's in CHH context: 131931841 Total unmethylated C's in Unknown context: 3982989 C methylated in CpG context: 73.2% C methylated in CHG context: 8.5% C methylated in CHH context: 20.9% C methylated in unknown context (CN or CHN): 33.5% Bismark completed in 0d 4h 5m 21s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' FastQ format assumed (by default) 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1024'): /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R1_val_1.fq.gz /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R2_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) Current working directory is: /gscratch/srlab/sr320/analyses/1024 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_3_s1_R1_val_1.fq.gz to zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file zr2096_3_s1_R1_val_1.fq.gz (29548753 sequences in total) Writing a G -> A converted version of the input file zr2096_3_s1_R2_val_2.fq.gz to zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file zr2096_3_s1_R2_val_2.fq.gz (29548753 sequences in total) Input files are zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_3_s1_R2_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1059:2153_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 TAATTTAAATAATTTTATATAAATNNNNNNNNNNNNNNNTATTTAAATTAAAAATTTAAATAAATTTTTTTAATTATTTA FFFFFFFFFFFFFFFFFFFFFFFF###############<<>> Writing bisulfite mapping results to zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R2_val_2.fq.gz Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1104:2918:23440_1:N:0:ACAGTG NC_035780.1 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 29548753 reads; of these: 29548753 (100.00%) were paired; of these: 18778470 (63.55%) aligned concordantly 0 times 3781092 (12.80%) aligned concordantly exactly 1 time 6989191 (23.65%) aligned concordantly >1 times 36.45% overall alignment rate 29548753 reads; of these: 29548753 (100.00%) were paired; of these: 18789262 (63.59%) aligned concordantly 0 times 3757038 (12.71%) aligned concordantly exactly 1 time 7002453 (23.70%) aligned concordantly >1 times 36.41% overall alignment rate Processed 29548753 sequences in total Successfully deleted the temporary files zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29548753 Number of paired-end alignments with a unique best hit: 10380653 Mapping efficiency: 35.1% Sequence pairs with no alignments under any condition: 15079334 Sequence pairs did not map uniquely: 4088766 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5195217 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5185435 ((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: 262116982 Total methylated C's in CpG context: 27411098 Total methylated C's in CHG context: 4352030 Total methylated C's in CHH context: 31743267 Total methylated C's in Unknown context: 1620528 Total unmethylated C's in CpG context: 7451747 Total unmethylated C's in CHG context: 47342719 Total unmethylated C's in CHH context: 143816121 Total unmethylated C's in Unknown context: 3735520 C methylated in CpG context: 78.6% C methylated in CHG context: 8.4% C methylated in CHH context: 18.1% C methylated in unknown context (CN or CHN): 30.3% Bismark completed in 0d 4h 8m 6s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' FastQ format assumed (by default) 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1024'): /gscratch/srlab/sr320/data/oakl/zr2096_4_s1_R1_val_1.fq.gz /gscratch/srlab/sr320/data/oakl/zr2096_4_s1_R2_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) Current working directory is: /gscratch/srlab/sr320/analyses/1024 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/oakl/zr2096_4_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_4_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_4_s1_R1_val_1.fq.gz to zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file zr2096_4_s1_R1_val_1.fq.gz (23970516 sequences in total) Writing a G -> A converted version of the input file zr2096_4_s1_R2_val_2.fq.gz to zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file zr2096_4_s1_R2_val_2.fq.gz (23970516 sequences in total) Input files are zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_4_s1_R2_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1343:2133_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 ATAGTGGTTGTTATGGAAATTAGNNNNNNNNNNNNNNNNNNNNNNNNNTGNANTNTTTTTATTAGAATTGTTAAGGTTT FFFFFFFFFFFFFFFFFFFFFFF#########################<<#<#/#<>> Writing bisulfite mapping results to zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/oakl/zr2096_4_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_4_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2114:3090:6243_1:N:0:GCCAAT NC_007175.2 17180 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2206:10235:74664_1:N:0:GCCAAT NC_007175.2 17189 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far 23970516 reads; of these: 23970516 (100.00%) were paired; of these: 14648788 (61.11%) aligned concordantly 0 times 3318165 (13.84%) aligned concordantly exactly 1 time 6003563 (25.05%) aligned concordantly >1 times 38.89% overall alignment rate 23970516 reads; of these: 23970516 (100.00%) were paired; of these: 14656622 (61.14%) aligned concordantly 0 times 3300076 (13.77%) aligned concordantly exactly 1 time 6013818 (25.09%) aligned concordantly >1 times 38.86% overall alignment rate Processed 23970516 sequences in total Successfully deleted the temporary files zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 23970516 Number of paired-end alignments with a unique best hit: 9089192 Mapping efficiency: 37.9% Sequence pairs with no alignments under any condition: 11418028 Sequence pairs did not map uniquely: 3463296 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4542529 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4546661 ((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: 209754854 Total methylated C's in CpG context: 16536709 Total methylated C's in CHG context: 3089119 Total methylated C's in CHH context: 27361672 Total methylated C's in Unknown context: 1448730 Total unmethylated C's in CpG context: 7574325 Total unmethylated C's in CHG context: 36518995 Total unmethylated C's in CHH context: 118674034 Total unmethylated C's in Unknown context: 3304723 C methylated in CpG context: 68.6% C methylated in CHG context: 7.8% C methylated in CHH context: 18.7% C methylated in unknown context (CN or CHN): 30.5% Bismark completed in 0d 3h 28m 56s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' FastQ format assumed (by default) 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1024'): /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R1_val_1.fq.gz /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R2_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) Current working directory is: /gscratch/srlab/sr320/analyses/1024 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_5_s1_R1_val_1.fq.gz to zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file zr2096_5_s1_R1_val_1.fq.gz (31503281 sequences in total) Writing a G -> A converted version of the input file zr2096_5_s1_R2_val_2.fq.gz to zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file zr2096_5_s1_R2_val_2.fq.gz (31503281 sequences in total) Input files are zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_5_s1_R2_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1218:2142_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TTATTTAAATTTTATTATTTATANNNNNNNNNNNNNNNNNNATTNTTTTTATTATATATATAAAATTATTTTAAAATTAT FFFFFFFFFFFFFFFFFFFFFFF##################<<<#<>> Writing bisulfite mapping results to zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1204:19985:42416_1:N:0:CAGATC NC_007175.2 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far 31503281 reads; of these: 31503281 (100.00%) were paired; of these: 20448378 (64.91%) aligned concordantly 0 times 4092366 (12.99%) aligned concordantly exactly 1 time 6962537 (22.10%) aligned concordantly >1 times 35.09% overall alignment rate 31503281 reads; of these: 31503281 (100.00%) were paired; of these: 20454094 (64.93%) aligned concordantly 0 times 4100089 (13.01%) aligned concordantly exactly 1 time 6949098 (22.06%) aligned concordantly >1 times 35.07% overall alignment rate Processed 31503281 sequences in total Successfully deleted the temporary files zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 31503281 Number of paired-end alignments with a unique best hit: 11081867 Mapping efficiency: 35.2% Sequence pairs with no alignments under any condition: 16450305 Sequence pairs did not map uniquely: 3971109 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5546840 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5535026 ((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: 268342231 Total methylated C's in CpG context: 21594751 Total methylated C's in CHG context: 3967717 Total methylated C's in CHH context: 32353960 Total methylated C's in Unknown context: 1739639 Total unmethylated C's in CpG context: 9342682 Total unmethylated C's in CHG context: 46640152 Total unmethylated C's in CHH context: 154442969 Total unmethylated C's in Unknown context: 4146922 C methylated in CpG context: 69.8% C methylated in CHG context: 7.8% C methylated in CHH context: 17.3% C methylated in unknown context (CN or CHN): 29.6% Bismark completed in 0d 4h 23m 12s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' FastQ format assumed (by default) 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1024'): /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R1_val_1.fq.gz /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R2_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) Current working directory is: /gscratch/srlab/sr320/analyses/1024 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_6_s1_R1_val_1.fq.gz to zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file zr2096_6_s1_R1_val_1.fq.gz (23909493 sequences in total) Writing a G -> A converted version of the input file zr2096_6_s1_R2_val_2.fq.gz to zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file zr2096_6_s1_R2_val_2.fq.gz (23909493 sequences in total) Input files are zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_6_s1_R2_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1093:2134_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 TTAATTTTATTATTAAATAAAAANNNNNNNNNNNNNNNNNNNNNNANNTANANAAATATTAATTAAATATTTTTAAAATA FFFFFFFFFFFFFFFFFFFFFFF######################<##<<#<#<>> Writing bisulfite mapping results to zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1201:7258:96604_1:N:0:CTTGTA NC_035780.1 1 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far 23909493 reads; of these: 23909493 (100.00%) were paired; of these: 14498117 (60.64%) aligned concordantly 0 times 3348540 (14.01%) aligned concordantly exactly 1 time 6062836 (25.36%) aligned concordantly >1 times 39.36% overall alignment rate 23909493 reads; of these: 23909493 (100.00%) were paired; of these: 14494359 (60.62%) aligned concordantly 0 times 3360537 (14.06%) aligned concordantly exactly 1 time 6054597 (25.32%) aligned concordantly >1 times 39.38% overall alignment rate Processed 23909493 sequences in total Successfully deleted the temporary files zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 23909493 Number of paired-end alignments with a unique best hit: 9156061 Mapping efficiency: 38.3% Sequence pairs with no alignments under any condition: 11217257 Sequence pairs did not map uniquely: 3536175 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4581940 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4574120 ((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: 215726634 Total methylated C's in CpG context: 19251070 Total methylated C's in CHG context: 3244170 Total methylated C's in CHH context: 26801491 Total methylated C's in Unknown context: 1418728 Total unmethylated C's in CpG context: 6469270 Total unmethylated C's in CHG context: 37877713 Total unmethylated C's in CHH context: 122082920 Total unmethylated C's in Unknown context: 3369200 C methylated in CpG context: 74.8% C methylated in CHG context: 7.9% C methylated in CHH context: 18.0% C methylated in unknown context (CN or CHN): 29.6% Bismark completed in 0d 3h 30m 56s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' FastQ format assumed (by default) 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1024'): /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R1_val_1.fq.gz /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R2_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) Current working directory is: /gscratch/srlab/sr320/analyses/1024 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_7_s1_R1_val_1.fq.gz to zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file zr2096_7_s1_R1_val_1.fq.gz (29273635 sequences in total) Writing a G -> A converted version of the input file zr2096_7_s1_R2_val_2.fq.gz to zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file zr2096_7_s1_R2_val_2.fq.gz (29273635 sequences in total) Input files are zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TTATTATGATGAATTTAAATATTAATAATAAAATTTAAAAAAAATATAAATGTTAAATATTAAATTTTTTAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 TTTTTAAAAAATTTAATATTTAACATTTATATTTTTTTTAAATTTTATTATTAATATTTAAATTCATCATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TTATTATGATGAATTTAAATATTAATAATAAAATTTAAAAAAAATATAAATGTTAAATATTAAATTTTTTAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 TTTTTAAAAAATTTAATATTTAACATTTATATTTTTTTTAAATTTTATTATTAATATTTAAATTCATCATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1316:19155:63509_1:N:0:ATCACG NC_007175.2 17169 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2209:9828:53780_1:N:0:ATCACG NC_007175.2 17175 Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2211:12726:18562_1:N:0:ATCACG NC_007175.2 17178 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2309:5099:43290_1:N:0:ATCACG NC_035788.1 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2310:2897:70225_1:N:0:ATCACG NC_007175.2 17178 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 29273635 reads; of these: 29273635 (100.00%) were paired; of these: 19540916 (66.75%) aligned concordantly 0 times 3691154 (12.61%) aligned concordantly exactly 1 time 6041565 (20.64%) aligned concordantly >1 times 33.25% overall alignment rate 29273635 reads; of these: 29273635 (100.00%) were paired; of these: 19534951 (66.73%) aligned concordantly 0 times 3703479 (12.65%) aligned concordantly exactly 1 time 6035205 (20.62%) aligned concordantly >1 times 33.27% overall alignment rate Processed 29273635 sequences in total Successfully deleted the temporary files zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29273635 Number of paired-end alignments with a unique best hit: 9890725 Mapping efficiency: 33.8% Sequence pairs with no alignments under any condition: 15885567 Sequence pairs did not map uniquely: 3497343 Sequence pairs which were discarded because genomic sequence could not be extracted: 5 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4949920 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4940800 ((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: 246786181 Total methylated C's in CpG context: 21427638 Total methylated C's in CHG context: 3894914 Total methylated C's in CHH context: 29362171 Total methylated C's in Unknown context: 1435538 Total unmethylated C's in CpG context: 7561338 Total unmethylated C's in CHG context: 44030117 Total unmethylated C's in CHH context: 140510003 Total unmethylated C's in Unknown context: 3589407 C methylated in CpG context: 73.9% C methylated in CHG context: 8.1% C methylated in CHH context: 17.3% C methylated in unknown context (CN or CHN): 28.6% Bismark completed in 0d 4h 1m 33s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' FastQ format assumed (by default) 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1024'): /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R1_val_1.fq.gz /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R2_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) Current working directory is: /gscratch/srlab/sr320/analyses/1024 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_8_s1_R1_val_1.fq.gz to zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file zr2096_8_s1_R1_val_1.fq.gz (29483218 sequences in total) Writing a G -> A converted version of the input file zr2096_8_s1_R2_val_2.fq.gz to zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file zr2096_8_s1_R2_val_2.fq.gz (29483218 sequences in total) Input files are zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_8_s1_R2_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1281:2170_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 TTAAAAAATTTATTAAATTTATTATTATTTNTTATTTTTTATAAAAGAAAATAGAGAGAGAGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#<>> Writing bisulfite mapping results to zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1105:1822:7304_1:N:0:TTAGGC NC_007175.2 17173 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1301:18980:18166_1:Y:0:TTAGGC NC_007175.2 17175 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1311:7196:8646_1:N:0:TTAGGC NC_007175.2 1 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2209:16412:85480_1:N:0:TTAGGC NC_007175.2 17173 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2315:4342:46624_1:N:0:TTAGGC NC_007175.2 17187 Processed 29000000 sequence pairs so far 29483218 reads; of these: 29483218 (100.00%) were paired; of these: 20226572 (68.60%) aligned concordantly 0 times 3503325 (11.88%) aligned concordantly exactly 1 time 5753321 (19.51%) aligned concordantly >1 times 31.40% overall alignment rate 29483218 reads; of these: 29483218 (100.00%) were paired; of these: 20209983 (68.55%) aligned concordantly 0 times 3511012 (11.91%) aligned concordantly exactly 1 time 5762223 (19.54%) aligned concordantly >1 times 31.45% overall alignment rate Processed 29483218 sequences in total Successfully deleted the temporary files zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29483218 Number of paired-end alignments with a unique best hit: 9407795 Mapping efficiency: 31.9% Sequence pairs with no alignments under any condition: 16770677 Sequence pairs did not map uniquely: 3304746 Sequence pairs which were discarded because genomic sequence could not be extracted: 5 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4715916 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4691874 ((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: 225610655 Total methylated C's in CpG context: 17168213 Total methylated C's in CHG context: 3453150 Total methylated C's in CHH context: 28820105 Total methylated C's in Unknown context: 1493571 Total unmethylated C's in CpG context: 7733254 Total unmethylated C's in CHG context: 39574096 Total unmethylated C's in CHH context: 128861837 Total unmethylated C's in Unknown context: 3462826 C methylated in CpG context: 68.9% C methylated in CHG context: 8.0% C methylated in CHH context: 18.3% C methylated in unknown context (CN or CHN): 30.1% Bismark completed in 0d 3h 56m 40s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' FastQ format assumed (by default) 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1024'): /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R1_val_1.fq.gz /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R2_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) Current working directory is: /gscratch/srlab/sr320/analyses/1024 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_9_s1_R1_val_1.fq.gz to zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file zr2096_9_s1_R1_val_1.fq.gz (31847541 sequences in total) Writing a G -> A converted version of the input file zr2096_9_s1_R2_val_2.fq.gz to zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file zr2096_9_s1_R2_val_2.fq.gz (31847541 sequences in total) Input files are zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_9_s1_R2_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:2:1101:1135:2128_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AAAATAATAAATAATAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >> Writing bisulfite mapping results to zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:2213:18183:81000_1:N:0:ACTTGA NC_007175.2 17188 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:2312:18012:97005_1:N:0:ACTTGA NC_007175.2 17168 Processed 31000000 sequence pairs so far 31847541 reads; of these: 31847541 (100.00%) were paired; of these: 20693107 (64.98%) aligned concordantly 0 times 4162334 (13.07%) aligned concordantly exactly 1 time 6992100 (21.95%) aligned concordantly >1 times 35.02% overall alignment rate 31847541 reads; of these: 31847541 (100.00%) were paired; of these: 20682023 (64.94%) aligned concordantly 0 times 4189365 (13.15%) aligned concordantly exactly 1 time 6976153 (21.90%) aligned concordantly >1 times 35.06% overall alignment rate Processed 31847541 sequences in total Successfully deleted the temporary files zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 31847541 Number of paired-end alignments with a unique best hit: 11022655 Mapping efficiency: 34.6% Sequence pairs with no alignments under any condition: 16603362 Sequence pairs did not map uniquely: 4221524 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5511907 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5510746 ((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: 283742007 Total methylated C's in CpG context: 29218698 Total methylated C's in CHG context: 4113011 Total methylated C's in CHH context: 28392736 Total methylated C's in Unknown context: 1610043 Total unmethylated C's in CpG context: 8269630 Total unmethylated C's in CHG context: 52973382 Total unmethylated C's in CHH context: 160774550 Total unmethylated C's in Unknown context: 4139758 C methylated in CpG context: 77.9% C methylated in CHG context: 7.2% C methylated in CHH context: 15.0% C methylated in unknown context (CN or CHN): 28.0% Bismark completed in 0d 4h 24m 43s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_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 >>/gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam: 6101640 Total number duplicated alignments removed: 234688 (3.85%) Duplicated alignments were found at: 184512 different position(s) Total count of deduplicated leftover sequences: 5866952 (96.15% of total) Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R2_val_2.fq.gz" Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam: 5210641 Total number duplicated alignments removed: 602416 (11.56%) Duplicated alignments were found at: 202112 different position(s) Total count of deduplicated leftover sequences: 4608225 (88.44% of total) Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R2_val_2.fq.gz" Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam: 10644442 Total number duplicated alignments removed: 799246 (7.51%) Duplicated alignments were found at: 478060 different position(s) Total count of deduplicated leftover sequences: 9845196 (92.49% of total) Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R2_val_2.fq.gz" Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam: 10380652 Total number duplicated alignments removed: 529782 (5.10%) Duplicated alignments were found at: 381758 different position(s) Total count of deduplicated leftover sequences: 9850870 (94.90% of total) Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R2_val_2.fq.gz" Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam: 9089190 Total number duplicated alignments removed: 273122 (3.00%) Duplicated alignments were found at: 207670 different position(s) Total count of deduplicated leftover sequences: 8816068 (97.00% of total) Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_4_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_4_s1_R2_val_2.fq.gz" Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam: 11081866 Total number duplicated alignments removed: 627908 (5.67%) Duplicated alignments were found at: 477425 different position(s) Total count of deduplicated leftover sequences: 10453958 (94.33% of total) Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R2_val_2.fq.gz" Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam: 9156060 Total number duplicated alignments removed: 306451 (3.35%) Duplicated alignments were found at: 229020 different position(s) Total count of deduplicated leftover sequences: 8849609 (96.65% of total) Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R2_val_2.fq.gz" Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam: 9890720 Total number duplicated alignments removed: 379722 (3.84%) Duplicated alignments were found at: 299444 different position(s) Total count of deduplicated leftover sequences: 9510998 (96.16% of total) Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R2_val_2.fq.gz" Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam: 9407790 Total number duplicated alignments removed: 526486 (5.60%) Duplicated alignments were found at: 360199 different position(s) Total count of deduplicated leftover sequences: 8881304 (94.40% of total) Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R2_val_2.fq.gz" Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam: 11022653 Total number duplicated alignments removed: 1419260 (12.88%) Duplicated alignments were found at: 1129621 different position(s) Total count of deduplicated leftover sequences: 9603393 (87.12% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R2_val_2.fq.gz" *** Bismark methylation extractor version v0.19.0 *** Trying to determine the type of mapping from the SAM header line of file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/srlab/sr320/analyses/1024') 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: '2G'. Temporary directory used for sorting is the output directory Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_10_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 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.. Merging individual splitting reports into overall report: 'zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 5866952 lines in total Total number of methylation call strings processed: 11733904 Final Cytosine Methylation Report ================================= Total number of C's analysed: 97475823 Total methylated C's in CpG context: 9026043 Total methylated C's in CHG context: 1538925 Total methylated C's in CHH context: 10243338 Total C to T conversions in CpG context: 3636169 Total C to T conversions in CHG context: 18001224 Total C to T conversions in CHH context: 55030124 C methylated in CpG context: 71.3% C methylated in CHG context: 7.9% C methylated in CHH context: 15.7% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 80 Maximum read length of Read 2: 80 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: 80 Maximum read length of Read 2: 80 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr2096_10_s1_R1_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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1024/CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/srlab/sr320/analyses/1024/CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_1_s1_R1_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:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_1_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Finished processing child process. Exiting.. Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Finished processing child process. Exiting.. Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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: 'zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 4608225 lines in total Total number of methylation call strings processed: 9216450 Final Cytosine Methylation Report ================================= Total number of C's analysed: 72332983 Total methylated C's in CpG context: 6025223 Total methylated C's in CHG context: 1114246 Total methylated C's in CHH context: 8658535 Total C to T conversions in CpG context: 2420764 Total C to T conversions in CHG context: 12288170 Total C to T conversions in CHH context: 41826045 C methylated in CpG context: 71.3% C methylated in CHG context: 8.3% C methylated in CHH context: 17.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 80 Maximum read length of Read 2: 80 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: 80 Maximum read length of Read 2: 80 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr2096_1_s1_R1_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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1024/CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/srlab/sr320/analyses/1024/CpG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_2_s1_R1_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:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_2_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9845196 lines in total Total number of methylation call strings processed: 19690392 Final Cytosine Methylation Report ================================= Total number of C's analysed: 136229712 Total methylated C's in CpG context: 11879226 Total methylated C's in CHG context: 2157657 Total methylated C's in CHH context: 17634457 Total C to T conversions in CpG context: 4507158 Total C to T conversions in CHG context: 24233929 Total C to T conversions in CHH context: 75817285 C methylated in CpG context: 72.5% C methylated in CHG context: 8.2% C methylated in CHH context: 18.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 80 Maximum read length of Read 2: 80 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: 80 Maximum read length of Read 2: 80 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr2096_2_s1_R1_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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1024/CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/srlab/sr320/analyses/1024/CpG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_3_s1_R1_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:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_3_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9850870 lines in total Total number of methylation call strings processed: 19701740 Final Cytosine Methylation Report ================================= Total number of C's analysed: 160911412 Total methylated C's in CpG context: 16847360 Total methylated C's in CHG context: 2616555 Total methylated C's in CHH context: 17387198 Total C to T conversions in CpG context: 4726865 Total C to T conversions in CHG context: 29584213 Total C to T conversions in CHH context: 89749221 C methylated in CpG context: 78.1% C methylated in CHG context: 8.1% C methylated in CHH context: 16.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 80 Maximum read length of Read 2: 80 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: 80 Maximum read length of Read 2: 80 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr2096_3_s1_R1_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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1024/CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/srlab/sr320/analyses/1024/CpG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_4_s1_R1_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:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_4_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_4_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8816068 lines in total Total number of methylation call strings processed: 17632136 Final Cytosine Methylation Report ================================= Total number of C's analysed: 126313155 Total methylated C's in CpG context: 9972224 Total methylated C's in CHG context: 1848398 Total methylated C's in CHH context: 14890081 Total C to T conversions in CpG context: 4727011 Total C to T conversions in CHG context: 22432587 Total C to T conversions in CHH context: 72442854 C methylated in CpG context: 67.8% C methylated in CHG context: 7.6% C methylated in CHH context: 17.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 80 Maximum read length of Read 2: 80 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: 80 Maximum read length of Read 2: 80 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr2096_4_s1_R1_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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1024/CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/srlab/sr320/analyses/1024/CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_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 /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_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 /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_5_s1_R1_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:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_5_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 10453958 lines in total Total number of methylation call strings processed: 20907916 Final Cytosine Methylation Report ================================= Total number of C's analysed: 161268048 Total methylated C's in CpG context: 12900369 Total methylated C's in CHG context: 2345195 Total methylated C's in CHH context: 17389225 Total C to T conversions in CpG context: 5831349 Total C to T conversions in CHG context: 28452905 Total C to T conversions in CHH context: 94349005 C methylated in CpG context: 68.9% C methylated in CHG context: 7.6% C methylated in CHH context: 15.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 80 Maximum read length of Read 2: 80 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: 80 Maximum read length of Read 2: 80 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr2096_5_s1_R1_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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1024/CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/srlab/sr320/analyses/1024/CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_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 /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_6_s1_R1_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:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_6_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8849609 lines in total Total number of methylation call strings processed: 17699218 Final Cytosine Methylation Report ================================= Total number of C's analysed: 130205684 Total methylated C's in CpG context: 11634357 Total methylated C's in CHG context: 1936357 Total methylated C's in CHH context: 14566048 Total C to T conversions in CpG context: 4045934 Total C to T conversions in CHG context: 23280878 Total C to T conversions in CHH context: 74742110 C methylated in CpG context: 74.2% C methylated in CHG context: 7.7% C methylated in CHH context: 16.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 80 Maximum read length of Read 2: 80 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: 80 Maximum read length of Read 2: 80 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr2096_6_s1_R1_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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1024/CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/srlab/sr320/analyses/1024/CpG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_7_s1_R1_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:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_7_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Finished processing child process. Exiting.. Processed lines: 9500000 Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9510998 lines in total Total number of methylation call strings processed: 19021996 Final Cytosine Methylation Report ================================= Total number of C's analysed: 155753265 Total methylated C's in CpG context: 13485481 Total methylated C's in CHG context: 2435141 Total methylated C's in CHH context: 16681466 Total C to T conversions in CpG context: 4922686 Total C to T conversions in CHG context: 28205376 Total C to T conversions in CHH context: 90023115 C methylated in CpG context: 73.3% C methylated in CHG context: 7.9% C methylated in CHH context: 15.6% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 80 Maximum read length of Read 2: 80 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: 80 Maximum read length of Read 2: 80 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr2096_7_s1_R1_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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1024/CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/srlab/sr320/analyses/1024/CpG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_8_s1_R1_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:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_8_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. 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: 'zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 8881304 lines in total Total number of methylation call strings processed: 17762608 Final Cytosine Methylation Report ================================= Total number of C's analysed: 138668831 Total methylated C's in CpG context: 10553263 Total methylated C's in CHG context: 2096807 Total methylated C's in CHH context: 15783174 Total C to T conversions in CpG context: 4900827 Total C to T conversions in CHG context: 24826006 Total C to T conversions in CHH context: 80508754 C methylated in CpG context: 68.3% C methylated in CHG context: 7.8% C methylated in CHH context: 16.4% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 80 Maximum read length of Read 2: 80 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: 80 Maximum read length of Read 2: 80 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr2096_8_s1_R1_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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1024/CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/srlab/sr320/analyses/1024/CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1024/zr2096_9_s1_R1_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:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-1.2 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 -1 /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/oakl/zr2096_9_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Finished 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: 'zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 9603393 lines in total Total number of methylation call strings processed: 19206786 Final Cytosine Methylation Report ================================= Total number of C's analysed: 158911121 Total methylated C's in CpG context: 16104320 Total methylated C's in CHG context: 2309337 Total methylated C's in CHH context: 14720410 Total C to T conversions in CpG context: 4779650 Total C to T conversions in CHG context: 29739238 Total C to T conversions in CHH context: 91258166 C methylated in CpG context: 77.1% C methylated in CHG context: 7.2% C methylated in CHH context: 13.9% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 80 Maximum read length of Read 2: 80 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: 80 Maximum read length of Read 2: 80 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr2096_9_s1_R1_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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1024/CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/srlab/sr320/analyses/1024/CpG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 10 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_9_s1_R1_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/Bowtie single-end BAM files detected No Bismark/Bowtie paired-end BAM files detected Generating Bismark summary report from 10 Bismark BAM file(s)... >> Reading from Bismark report: zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks...