*** 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-Subset')


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 -u 10000 --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"
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_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 2085 lines in total
Total number of methylation call strings processed: 4170

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	37255

Total methylated C's in CpG context:	4153
Total methylated C's in CHG context:	138
Total methylated C's in CHH context:	390

Total C to T conversions in CpG context:	1243
Total C to T conversions in CHG context:	8570
Total C to T conversions in CHH context:	22761

C methylated in CpG context:	77.0%
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_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

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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 -u 10000 --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"
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..

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

Processed 816 lines in total
Total number of methylation call strings processed: 1632

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	14383

Total methylated C's in CpG context:	1546
Total methylated C's in CHG context:	38
Total methylated C's in CHH context:	125

Total C to T conversions in CpG context:	411
Total C to T conversions in CHG context:	3270
Total C to T conversions in CHH context:	8993

C methylated in CpG context:	79.0%
C methylated in CHG context:	1.1%
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_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


Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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

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 -u 10000 --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"
Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Now waiting for all child processes to complete
Finished processing child process. Exiting..

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

Processed 1914 lines in total
Total number of methylation call strings processed: 3828

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	28880

Total methylated C's in CpG context:	3219
Total methylated C's in CHG context:	108
Total methylated C's in CHH context:	343

Total C to T conversions in CpG context:	919
Total C to T conversions in CHG context:	6740
Total C to T conversions in CHH context:	17551

C methylated in CpG context:	77.8%
C methylated in CHG context:	1.6%
C methylated in CHH context:	1.9%



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

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --non_directional -p 4 -u 10000 --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"
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..

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

Processed 2144 lines in total
Total number of methylation call strings processed: 4288

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	36853

Total methylated C's in CpG context:	4674
Total methylated C's in CHG context:	108
Total methylated C's in CHH context:	333

Total C to T conversions in CpG context:	888
Total C to T conversions in CHG context:	8450
Total C to T conversions in CHH context:	22400

C methylated in CpG context:	84.0%
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_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

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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 -u 10000 --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"
Finished processing child process. Exiting..
Now waiting for all child processes to complete
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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 2104 lines in total
Total number of methylation call strings processed: 4208

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	33141

Total methylated C's in CpG context:	3371
Total methylated C's in CHG context:	94
Total methylated C's in CHH context:	341

Total C to T conversions in CpG context:	1132
Total C to T conversions in CHG context:	7504
Total C to T conversions in CHH context:	20699

C methylated in CpG context:	74.9%
C methylated in CHG context:	1.2%
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_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

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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 -u 10000 --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"
Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Now waiting for all child processes to complete

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

Processed 1996 lines in total
Total number of methylation call strings processed: 3992

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	33583

Total methylated C's in CpG context:	3363
Total methylated C's in CHG context:	126
Total methylated C's in CHH context:	332

Total C to T conversions in CpG context:	1092
Total C to T conversions in CHG context:	7361
Total C to T conversions in CHH context:	21309

C methylated in CpG context:	75.5%
C methylated in CHG context:	1.7%
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_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


Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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 -u 10000 --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"
Finished processing child process. Exiting..
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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 2184 lines in total
Total number of methylation call strings processed: 4368

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	34036

Total methylated C's in CpG context:	3957
Total methylated C's in CHG context:	91
Total methylated C's in CHH context:	325

Total C to T conversions in CpG context:	831
Total C to T conversions in CHG context:	7779
Total C to T conversions in CHH context:	21053

C methylated in CpG context:	82.6%
C methylated in CHG context:	1.2%
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

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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 -u 10000 --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"
Now waiting for all child processes to complete
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..

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 1930 lines in total
Total number of methylation call strings processed: 3860

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	32700

Total methylated C's in CpG context:	3415
Total methylated C's in CHG context:	123
Total methylated C's in CHH context:	329

Total C to T conversions in CpG context:	836
Total C to T conversions in CHG context:	7277
Total C to T conversions in CHH context:	20720

C methylated in CpG context:	80.3%
C methylated in CHG context:	1.7%
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_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

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.
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 -u 10000 --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"
Now waiting for all child processes to complete
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..

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 1802 lines in total
Total number of methylation call strings processed: 3604

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	29661

Total methylated C's in CpG context:	2847
Total methylated C's in CHG context:	94
Total methylated C's in CHH context:	391

Total C to T conversions in CpG context:	962
Total C to T conversions in CHG context:	6761
Total C to T conversions in CHH context:	18606

C methylated in CpG context:	74.7%
C methylated in CHG context:	1.4%
C methylated in CHH context:	2.1%



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

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

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 -u 10000 --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"
Finished processing child process. Exiting..
Now waiting for all child processes to complete
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..

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 1890 lines in total
Total number of methylation call strings processed: 3780

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	32674

Total methylated C's in CpG context:	4036
Total methylated C's in CHG context:	157
Total methylated C's in CHH context:	332

Total C to T conversions in CpG context:	792
Total C to T conversions in CHG context:	7478
Total C to T conversions in CHH context:	19879

C methylated in CpG context:	83.6%
C methylated in CHG context:	2.1%
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_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 ...