*** Bismark methylation extractor version v0.19.0 ***

Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark paired-end SAM format specified (default)
Number of cores to be used: 2
Output will be written to the current directory ('/Volumes/Serine/wd/18-04-12/tmp2')


Summarising bedGraph parameters:
===============================================================
Generating additional output in bedGraph and coverage format
bedGraph format:	<Chromosome> <Start Position> <End Position> <Methylation Percentage>
coverage format:	<Chromosome> <Start Position> <End Position> <Methylation Percentage> <count methylated> <count non-methylated>

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_6_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_6_s1_R1_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_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_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_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_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_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_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_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_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_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_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_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bam

skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 --genome /Volumes/Serine/wd/18-03-15/genome --score_min L,0,-1.2 -u 10000 -p 4 --non_directional -1 /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R1.fastq.gz -2 /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R2.fastq.gz"
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: 'zr2096_6_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 5632 lines in total
Total number of methylation call strings processed: 11264

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	108650

Total methylated C's in CpG context:	10639
Total methylated C's in CHG context:	779
Total methylated C's in CHH context:	2887

Total C to T conversions in CpG context:	4016
Total C to T conversions in CHG context:	23630
Total C to T conversions in CHH context:	66699

C methylated in CpG context:	72.6%
C methylated in CHG context:	3.2%
C methylated in CHH context:	4.1%



Merging individual M-bias reports into overall M-bias statistics from these 2 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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: 100
Maximum read length of Read 2: 100

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_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_6_s1_R1_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_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Applications/bioinfo/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...