*** Bismark methylation extractor version v0.19.0 *** Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Core usage currently set to more than 20 threads. Let's see how this goes... (set value: 28) Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 28 Output will be written to the current directory ('/gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools') 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... Now testing Bismark result file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 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 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 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 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 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 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 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 /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_10_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_10_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 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Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Processed lines: 8500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 8959633 lines in total Total number of methylation call strings processed: 17919266 Final Cytosine Methylation Report ================================= Total number of C's analysed: 162550688 Total methylated C's in CpG context: 15623053 Total methylated C's in CHG context: 964793 Total methylated C's in CHH context: 4172504 Total C to T conversions in CpG context: 6899821 Total C to T conversions in CHG context: 34745591 Total C to T conversions in CHH context: 100144926 C methylated in CpG context: 69.4% 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 28 individual files: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 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: /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_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... Now testing Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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 Now reading in Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_1_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_1_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 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Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Finished processing child process. Exiting.. Processed lines: 7000000 Finished processing child process. Exiting.. Processed lines: 7000000 Processed lines: 7000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 7000000 Processed lines: 7000000 Finished processing child process. Exiting.. Processed lines: 7000000 Processed lines: 7000000 Finished processing child process. Exiting.. Processed lines: 7000000 Finished processing child process. Exiting.. Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 7278446 lines in total Total number of methylation call strings processed: 14556892 Final Cytosine Methylation Report ================================= Total number of C's analysed: 122983889 Total methylated C's in CpG context: 10626266 Total methylated C's in CHG context: 804585 Total methylated C's in CHH context: 6097998 Total C to T conversions in CpG context: 4577584 Total C to T conversions in CHG context: 24001874 Total C to T conversions in CHH context: 76875582 C methylated in CpG context: 69.9% C methylated in CHG context: 3.2% C methylated in CHH context: 7.3% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 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: /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_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... Now testing Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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 Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_2_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_2_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 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Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 13500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13500000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 14000000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 14000000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Finished processing child process. Exiting.. Processed lines: 13500000 Finished processing child process. Exiting.. Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 13500000 Processed lines: 13500000 Finished processing child process. Exiting.. Processed lines: 13500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 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_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 14119992 lines in total Total number of methylation call strings processed: 28239984 Final Cytosine Methylation Report ================================= Total number of C's analysed: 217855622 Total methylated C's in CpG context: 20356245 Total methylated C's in CHG context: 1293967 Total methylated C's in CHH context: 8161912 Total C to T conversions in CpG context: 8346961 Total C to T conversions in CHG context: 46525869 Total C to T conversions in CHH context: 133170668 C methylated in CpG context: 70.9% C methylated in CHG context: 2.7% C methylated in CHH context: 5.8% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 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: /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_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... Now testing Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_3_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_3_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 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lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14500000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14000000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14000000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14000000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14500000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 14807502 lines in total Total number of methylation call strings processed: 29615004 Final Cytosine Methylation Report ================================= Total number of C's analysed: 267693368 Total methylated C's in CpG context: 29337022 Total methylated C's in CHG context: 1506507 Total methylated C's in CHH context: 6531799 Total C to T conversions in CpG context: 8890935 Total C to T conversions in CHG context: 57632709 Total C to T conversions in CHH context: 163794396 C methylated in CpG context: 76.7% 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 28 individual files: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 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: /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_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... Now testing Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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 /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_4_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_4_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 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lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Finished processing child process. Exiting.. Processed lines: 12000000 Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12000000 Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12500000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 12663182 lines in total Total number of methylation call strings processed: 25326364 Final Cytosine Methylation Report ================================= Total number of C's analysed: 202414211 Total methylated C's in CpG context: 16972342 Total methylated C's in CHG context: 1072413 Total methylated C's in CHH context: 5847499 Total C to T conversions in CpG context: 8759183 Total C to T conversions in CHG context: 42789465 Total C to T conversions in CHH context: 126973309 C methylated in CpG context: 66.0% C methylated in CHG context: 2.4% C methylated in CHH context: 4.4% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 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: /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_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... Now testing Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 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 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. 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. 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. Warning: unable to close filehandle IN properly. 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. 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. 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. 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. 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 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 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. 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. 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. 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 Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_5_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_5_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 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lines: 15000000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 14500000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 15000000 Processed lines: 15500000 Processed lines: 15000000 Finished processing child process. Exiting.. Processed lines: 15000000 Finished processing child process. Exiting.. Processed lines: 15000000 Processed lines: 15000000 Processed lines: 15500000 Processed lines: 15000000 Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 15500000 Processed lines: 15500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 15500000 Processed lines: 15000000 Finished processing child process. Exiting.. Processed lines: 15500000 Finished processing child process. Exiting.. Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Finished processing child process. Exiting.. Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 15500000 Processed lines: 15500000 Finished processing child process. Exiting.. Processed lines: 15500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 15500000 Processed lines: 15500000 Processed lines: 15500000 Finished processing child process. Exiting.. Processed lines: 15500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 15500000 Processed lines: 15500000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 15500000 Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 15535269 lines in total Total number of methylation call strings processed: 31070538 Final Cytosine Methylation Report ================================= Total number of C's analysed: 263351588 Total methylated C's in CpG context: 22025352 Total methylated C's in CHG context: 1491401 Total methylated C's in CHH context: 7586556 Total C to T conversions in CpG context: 10753176 Total C to T conversions in CHG context: 53978678 Total C to T conversions in CHH context: 167516425 C methylated in CpG context: 67.2% 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 28 individual files: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 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: /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_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... Now testing Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 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 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 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. 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. 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 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. 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. 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. 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. 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. 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. Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file 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 Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. 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. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_6_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_6_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 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Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12500000 Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Finished processing child process. Exiting.. Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 12500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 12648681 lines in total Total number of methylation call strings processed: 25297362 Final Cytosine Methylation Report ================================= Total number of C's analysed: 205670965 Total methylated C's in CpG context: 19494840 Total methylated C's in CHG context: 1103250 Total methylated C's in CHH context: 5783632 Total C to T conversions in CpG context: 7215123 Total C to T conversions in CHG context: 43323436 Total C to T conversions in CHH context: 128750684 C methylated in CpG context: 73.0% C methylated in CHG context: 2.5% C methylated in CHH context: 4.3% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 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: /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_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... Now testing Bismark result file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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 /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_7_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_7_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 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lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 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Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14500000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14500000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14500000 Processed lines: 14000000 Processed lines: 14500000 Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14500000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14500000 Processed lines: 14500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14500000 Processed lines: 14500000 Processed lines: 14500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14500000 Processed lines: 14500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14500000 Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Processed lines: 14500000 Processed lines: 14500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14500000 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_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 14617414 lines in total Total number of methylation call strings processed: 29234828 Final Cytosine Methylation Report ================================= Total number of C's analysed: 260442115 Total methylated C's in CpG context: 23405343 Total methylated C's in CHG context: 1551207 Total methylated C's in CHH context: 7056497 Total C to T conversions in CpG context: 9271729 Total C to T conversions in CHG context: 54544532 Total C to T conversions in CHH context: 164612807 C methylated in CpG context: 71.6% C methylated in CHG context: 2.8% C methylated in CHH context: 4.1% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 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: /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_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... Now testing Bismark result file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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 /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_8_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_8_s1_R2_val_2.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 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Exiting.. Finished processing child process. Exiting.. Processed lines: 13000000 Processed lines: 13000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Finished processing child process. Exiting.. Processed lines: 13000000 Finished processing child process. Exiting.. Processed lines: 13000000 Finished processing child process. Exiting.. Processed lines: 13000000 Finished processing child process. Exiting.. Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 13000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 13452841 lines in total Total number of methylation call strings processed: 26905682 Final Cytosine Methylation Report ================================= Total number of C's analysed: 228933398 Total methylated C's in CpG context: 18154221 Total methylated C's in CHG context: 1361580 Total methylated C's in CHH context: 7326787 Total C to T conversions in CpG context: 9182606 Total C to T conversions in CHG context: 47670865 Total C to T conversions in CHH context: 145237339 C methylated in CpG context: 66.4% C methylated in CHG context: 2.8% C methylated in CHH context: 4.8% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 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: /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_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... Now testing Bismark result file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --samtools_path /gscratch/srlab/programs/samtools-1.9/ --non_directional -p 28 -score_min L,0,-1.2 --genome /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-04-27-Bismark-Inputs/ -1 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_9_s1_R1_val_1.fq.gz -2 /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_9_s1_R2_val_2.fq.gz" 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. 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10000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 11500000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 11000000 Processed lines: 11000000 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lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 12000000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 12000000 Processed lines: 11500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 13000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13000000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13000000 Finished processing child process. Exiting.. Processed lines: 13500000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 13500000 Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 13500000 Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 13500000 Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14000000 Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 14000000 Processed lines: 14000000 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: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 14083414 lines in total Total number of methylation call strings processed: 28166828 Final Cytosine Methylation Report ================================= Total number of C's analysed: 255572824 Total methylated C's in CpG context: 26756008 Total methylated C's in CHG context: 1647018 Total methylated C's in CHH context: 7002283 Total C to T conversions in CpG context: 8438242 Total C to T conversions in CHG context: 54139076 Total C to T conversions in CHH context: 157590197 C methylated in CpG context: 76.0% C methylated in CHG context: 3.0% C methylated in CHH context: 4.3% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 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: /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/yaamini/analyses/Virginica-MBD/2018-10-31-Virginica-Bismark-Revised-Parameters-Samtools/CpG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_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 ... Found 10 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt < Processing alignment report zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/Bowtie single-end BAM files detected No Bismark/Bowtie paired-end BAM files detected Generating Bismark summary report from 10 Bismark BAM file(s)... >> Reading from Bismark report: zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html <<