*** 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: 8
Output will be written to the current directory ('/Users/yaamini/Documents/project-virginica-oa/analyses/2018-05-22-Bismark-Full-Samples')


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_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


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 --non_directional -p 4 --genome /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ -1 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_s1_R1_val_1.fq.gz -2 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_s1_R2_val_2.fq.gz"
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Finished 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_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 3434342 lines in total
Total number of methylation call strings processed: 6868684

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	60855875

Total methylated C's in CpG context:	6802392
Total methylated C's in CHG context:	224742
Total methylated C's in CHH context:	617812

Total C to T conversions in CpG context:	2072612
Total C to T conversions in CHG context:	13857622
Total C to T conversions in CHH context:	37280695

C methylated in CpG context:	76.6%
C methylated in CHG context:	1.6%
C methylated in CHH context:	1.6%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Deleting unused files ...

CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/Shared/Apps/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_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


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

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


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.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
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

skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
Warning: unable to close filehandle IN properly.
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 --non_directional -p 4 --genome /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ -1 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R1_val_1.fq.gz -2 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: 'zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 2226944 lines in total
Total number of methylation call strings processed: 4453888

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	39529814

Total methylated C's in CpG context:	4252678
Total methylated C's in CHG context:	121631
Total methylated C's in CHH context:	372137

Total C to T conversions in CpG context:	1129238
Total C to T conversions in CHG context:	8767791
Total C to T conversions in CHH context:	24886339

C methylated in CpG context:	79.0%
C methylated in CHG context:	1.4%
C methylated in CHH context:	1.5%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Deleting unused files ...

CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/Shared/Apps/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_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

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Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --non_directional -p 4 --genome /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ -1 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R1_val_1.fq.gz -2 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
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Now waiting for all child processes to complete
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Finished processing child process. Exiting..

Merging individual splitting reports into overall report: 'zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 5540986 lines in total
Total number of methylation call strings processed: 11081972

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	84341486

Total methylated C's in CpG context:	9405458
Total methylated C's in CHG context:	270517
Total methylated C's in CHH context:	836239

Total C to T conversions in CpG context:	2556396
Total C to T conversions in CHG context:	19722626
Total C to T conversions in CHH context:	51550250

C methylated in CpG context:	78.6%
C methylated in CHG context:	1.4%
C methylated in CHH context:	1.6%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Deleting unused files ...

CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/Shared/Apps/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_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

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Now reading in Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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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
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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 --non_directional -p 4 --genome /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ -1 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_s1_R1_val_1.fq.gz -2 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_s1_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
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Now waiting for all child processes to complete
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: 'zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 5787207 lines in total
Total number of methylation call strings processed: 11574414

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	101848268

Total methylated C's in CpG context:	12775527
Total methylated C's in CHG context:	324947
Total methylated C's in CHH context:	871626

Total C to T conversions in CpG context:	2506421
Total C to T conversions in CHG context:	23305151
Total C to T conversions in CHH context:	62064596

C methylated in CpG context:	83.6%
C methylated in CHG context:	1.4%
C methylated in CHH context:	1.4%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Deleting unused files ...

CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/Shared/Apps/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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.
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 --non_directional -p 4 --genome /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ -1 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_s1_R1_val_1.fq.gz -2 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_s1_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 5000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: 'zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 5026533 lines in total
Total number of methylation call strings processed: 10053066

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	77784040

Total methylated C's in CpG context:	7757276
Total methylated C's in CHG context:	237140
Total methylated C's in CHH context:	730836

Total C to T conversions in CpG context:	2714886
Total C to T conversions in CHG context:	17719197
Total C to T conversions in CHH context:	48624705

C methylated in CpG context:	74.1%
C methylated in CHG context:	1.3%
C methylated in CHH context:	1.5%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Deleting unused files ...

CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/Shared/Apps/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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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

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 --non_directional -p 4 --genome /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ -1 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R1_val_1.fq.gz -2 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: 'zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 5840204 lines in total
Total number of methylation call strings processed: 11680408

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	96381187

Total methylated C's in CpG context:	9568841
Total methylated C's in CHG context:	341342
Total methylated C's in CHH context:	1024051

Total C to T conversions in CpG context:	3132996
Total C to T conversions in CHG context:	21319450
Total C to T conversions in CHH context:	60994507

C methylated in CpG context:	75.3%
C methylated in CHG context:	1.6%
C methylated in CHH context:	1.7%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Deleting unused files ...

CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/Shared/Apps/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_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

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.
Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --non_directional -p 4 --genome /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ -1 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_s1_R1_val_1.fq.gz -2 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_s1_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: 'zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 4940751 lines in total
Total number of methylation call strings processed: 9881502

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	77489938

Total methylated C's in CpG context:	8738664
Total methylated C's in CHG context:	235438
Total methylated C's in CHH context:	712136

Total C to T conversions in CpG context:	1946085
Total C to T conversions in CHG context:	17600634
Total C to T conversions in CHH context:	48256981

C methylated in CpG context:	81.8%
C methylated in CHG context:	1.3%
C methylated in CHH context:	1.5%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Deleting unused files ...

CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/Shared/Apps/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_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


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.
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.

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 --non_directional -p 4 --genome /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ -1 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_7_s1_R1_val_1.fq.gz -2 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_7_s1_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: 'zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 5338007 lines in total
Total number of methylation call strings processed: 10676014

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	92316637

Total methylated C's in CpG context:	9708762
Total methylated C's in CHG context:	344182
Total methylated C's in CHH context:	996765

Total C to T conversions in CpG context:	2509696
Total C to T conversions in CHG context:	20669192
Total C to T conversions in CHH context:	58088040

C methylated in CpG context:	79.5%
C methylated in CHG context:	1.6%
C methylated in CHH context:	1.7%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Deleting unused files ...

CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/Shared/Apps/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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.
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 --non_directional -p 4 --genome /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ -1 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_s1_R1_val_1.fq.gz -2 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_s1_R2_val_2.fq.gz"
Processed lines: 500000
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Processed lines: 3500000
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Processed lines: 4000000
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Processed lines: 4500000
Processed lines: 4500000
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_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 4908453 lines in total
Total number of methylation call strings processed: 9816906

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	81716706

Total methylated C's in CpG context:	7694110
Total methylated C's in CHG context:	299912
Total methylated C's in CHH context:	925265

Total C to T conversions in CpG context:	2674951
Total C to T conversions in CHG context:	18378435
Total C to T conversions in CHH context:	51744033

C methylated in CpG context:	74.2%
C methylated in CHG context:	1.6%
C methylated in CHH context:	1.8%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Deleting unused files ...

CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/Shared/Apps/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr2096_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


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


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.
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 --non_directional -p 4 --genome /Users/yaamini/Documents/project-virginica-oa/analyses/2018-04-27-Bismark/2018-04-27-Bismark-Inputs/ -1 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_s1_R1_val_1.fq.gz -2 /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_s1_R2_val_2.fq.gz"
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Merging individual splitting reports into overall report: 'zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 5207356 lines in total
Total number of methylation call strings processed: 10414712

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	90111105

Total methylated C's in CpG context:	10936380
Total methylated C's in CHG context:	353176
Total methylated C's in CHH context:	964989

Total C to T conversions in CpG context:	2186658
Total C to T conversions in CHG context:	20344334
Total C to T conversions in CHH context:	55325568

C methylated in CpG context:	83.3%
C methylated in CHG context:	1.7%
C methylated in CHH context:	1.7%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 80
Maximum read length of Read 2: 80

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Deleting unused files ...

CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CpG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
CHH_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/Shared/Apps/Bismark_v0.19.0/bismark2bedGraph line 486.
Finished BedGraph conversion ...