*** Bismark methylation extractor version v0.19.0 *** 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: 4 Output will be written to the current directory ('/Volumes/Serine/wd/18-04-27') 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 >>zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... ...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 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 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 /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 1000000 -p 4 --non_directional -1 zr2096_10_s1_R1_val_1.fq.gz -2 zr2096_10_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 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_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Processed 530795 lines in total Total number of methylation call strings processed: 1061590 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9656656 Total methylated C's in CpG context: 932764 Total methylated C's in CHG context: 57156 Total methylated C's in CHH context: 243231 Total C to T conversions in CpG context: 407354 Total C to T conversions in CHG context: 2067121 Total C to T conversions in CHH context: 5949030 C methylated in CpG context: 69.6% C methylated in CHG context: 2.7% C methylated in CHH context: 3.9% Merging individual M-bias reports into overall M-bias statistics from these 4 individual files: 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 contains data -> kept CpG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHH_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_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_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_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_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_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: 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_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_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 >>zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 ...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 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 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 /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 1000000 -p 4 --non_directional -1 zr2096_1_s1_R1_val_1.fq.gz -2 zr2096_1_s1_R2_val_2.fq.gz" 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_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Processed 279330 lines in total Total number of methylation call strings processed: 558660 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4534552 Total methylated C's in CpG context: 385582 Total methylated C's in CHG context: 32257 Total methylated C's in CHH context: 275567 Total C to T conversions in CpG context: 164917 Total C to T conversions in CHG context: 864563 Total C to T conversions in CHH context: 2811666 C methylated in CpG context: 70.0% C methylated in CHG context: 3.6% C methylated in CHH context: 8.9% Merging individual M-bias reports into overall M-bias statistics from these 4 individual files: 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 contains data -> kept CpG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHH_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_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_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_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_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_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: 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_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_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 >>zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 ...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 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 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 /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 1000000 -p 4 --non_directional -1 zr2096_2_s1_R1_val_1.fq.gz -2 zr2096_2_s1_R2_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Processed 498118 lines in total Total number of methylation call strings processed: 996236 Final Cytosine Methylation Report ================================= Total number of C's analysed: 7583893 Total methylated C's in CpG context: 710832 Total methylated C's in CHG context: 45981 Total methylated C's in CHH context: 303174 Total C to T conversions in CpG context: 287332 Total C to T conversions in CHG context: 1613757 Total C to T conversions in CHH context: 4622817 C methylated in CpG context: 71.2% C methylated in CHG context: 2.8% C methylated in CHH context: 6.2% Merging individual M-bias reports into overall M-bias statistics from these 4 individual files: 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 contains data -> kept CpG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHH_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_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_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_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_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_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: 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_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_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 >>zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 ...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 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 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 /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 1000000 -p 4 --non_directional -1 zr2096_3_s1_R1_val_1.fq.gz -2 zr2096_3_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Processed 525048 lines in total Total number of methylation call strings processed: 1050096 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9507192 Total methylated C's in CpG context: 1049593 Total methylated C's in CHG context: 52867 Total methylated C's in CHH context: 226946 Total C to T conversions in CpG context: 312579 Total C to T conversions in CHG context: 2054583 Total C to T conversions in CHH context: 5810624 C methylated in CpG context: 77.1% C methylated in CHG context: 2.5% C methylated in CHH context: 3.8% Merging individual M-bias reports into overall M-bias statistics from these 4 individual files: 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 contains data -> kept CpG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHH_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_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_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_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_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_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: 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_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_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 >>zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 ...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 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 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 /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 1000000 -p 4 --non_directional -1 zr2096_4_s1_R1_val_1.fq.gz -2 zr2096_4_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Processed 540354 lines in total Total number of methylation call strings processed: 1080708 Final Cytosine Methylation Report ================================= Total number of C's analysed: 8656657 Total methylated C's in CpG context: 729965 Total methylated C's in CHG context: 45672 Total methylated C's in CHH context: 245765 Total C to T conversions in CpG context: 371588 Total C to T conversions in CHG context: 1834338 Total C to T conversions in CHH context: 5429329 C methylated in CpG context: 66.3% C methylated in CHG context: 2.4% C methylated in CHH context: 4.3% Merging individual M-bias reports into overall M-bias statistics from these 4 individual files: 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 contains data -> kept CpG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHH_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_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_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_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_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_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: 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_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_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 >>zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 ...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 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 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 /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 1000000 -p 4 --non_directional -1 zr2096_5_s1_R1_val_1.fq.gz -2 zr2096_5_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 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_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Processed 518859 lines in total Total number of methylation call strings processed: 1037718 Final Cytosine Methylation Report ================================= Total number of C's analysed: 8805499 Total methylated C's in CpG context: 743249 Total methylated C's in CHG context: 49454 Total methylated C's in CHH context: 250635 Total C to T conversions in CpG context: 355669 Total C to T conversions in CHG context: 1807852 Total C to T conversions in CHH context: 5598640 C methylated in CpG context: 67.6% C methylated in CHG context: 2.7% C methylated in CHH context: 4.3% Merging individual M-bias reports into overall M-bias statistics from these 4 individual files: 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 contains data -> kept CpG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHH_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_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_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_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_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_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: 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_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_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 >>zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 ...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 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 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 /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 1000000 -p 4 --non_directional -1 zr2096_6_s1_R1_val_1.fq.gz -2 zr2096_6_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Processed 544187 lines in total Total number of methylation call strings processed: 1088374 Final Cytosine Methylation Report ================================= Total number of C's analysed: 8865699 Total methylated C's in CpG context: 848156 Total methylated C's in CHG context: 47159 Total methylated C's in CHH context: 244710 Total C to T conversions in CpG context: 307232 Total C to T conversions in CHG context: 1874872 Total C to T conversions in CHH context: 5543570 C methylated in CpG context: 73.4% C methylated in CHG context: 2.5% C methylated in CHH context: 4.2% Merging individual M-bias reports into overall M-bias statistics from these 4 individual files: 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 contains data -> kept CpG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHH_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_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_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_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_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_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: 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_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_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 >>zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 ...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 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 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 /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 1000000 -p 4 --non_directional -1 zr2096_7_s1_R1_val_1.fq.gz -2 zr2096_7_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 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_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Processed 517334 lines in total Total number of methylation call strings processed: 1034668 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9248047 Total methylated C's in CpG context: 833778 Total methylated C's in CHG context: 54322 Total methylated C's in CHH context: 246563 Total C to T conversions in CpG context: 327574 Total C to T conversions in CHG context: 1940270 Total C to T conversions in CHH context: 5845540 C methylated in CpG context: 71.8% C methylated in CHG context: 2.7% C methylated in CHH context: 4.0% Merging individual M-bias reports into overall M-bias statistics from these 4 individual files: 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 contains data -> kept CpG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHH_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_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_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_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_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_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: 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_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_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 >>zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 ...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 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 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 /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 1000000 -p 4 --non_directional -1 zr2096_8_s1_R1_val_1.fq.gz -2 zr2096_8_s1_R2_val_2.fq.gz" 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_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Processed 479306 lines in total Total number of methylation call strings processed: 958612 Final Cytosine Methylation Report ================================= Total number of C's analysed: 8111311 Total methylated C's in CpG context: 644017 Total methylated C's in CHG context: 48503 Total methylated C's in CHH context: 271288 Total C to T conversions in CpG context: 323510 Total C to T conversions in CHG context: 1689076 Total C to T conversions in CHH context: 5134917 C methylated in CpG context: 66.6% C methylated in CHG context: 2.8% C methylated in CHH context: 5.0% Merging individual M-bias reports into overall M-bias statistics from these 4 individual files: 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 contains data -> kept CpG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHH_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_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_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_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_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_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: 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_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_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 >>zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 ...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 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 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 /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 1000000 -p 4 --non_directional -1 zr2096_9_s1_R1_val_1.fq.gz -2 zr2096_9_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 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_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: Processed 503808 lines in total Total number of methylation call strings processed: 1007616 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9143050 Total methylated C's in CpG context: 965361 Total methylated C's in CHG context: 58589 Total methylated C's in CHH context: 244429 Total C to T conversions in CpG context: 299089 Total C to T conversions in CHG context: 1948911 Total C to T conversions in CHH context: 5626671 C methylated in CpG context: 76.3% C methylated in CHG context: 2.9% C methylated in CHH context: 4.2% Merging individual M-bias reports into overall M-bias statistics from these 4 individual files: 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 contains data -> kept CpG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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 contains data -> kept CHH_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept 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_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_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_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_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_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_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: 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_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_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 ... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1